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Baek J, Yoon H. Cyclic di-GMP Modulates a Metabolic Flux for Carbon Utilization in Salmonella enterica Serovar Typhimurium. Microbiol Spectr 2023; 11:e0368522. [PMID: 36744926 PMCID: PMC10100716 DOI: 10.1128/spectrum.03685-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is an enteric pathogen spreading via the fecal-oral route. Transmission across humans, animals, and environmental reservoirs has forced this pathogen to rapidly respond to changing environments and adapt to new environmental conditions. Cyclic di-GMP (c-di-GMP) is a second messenger that controls the transition between planktonic and sessile lifestyles, in response to environmental cues. Our study reveals the potential of c-di-GMP to alter the carbon metabolic pathways in S. Typhimurium. Cyclic di-GMP overproduction decreased the transcription of genes that encode components of three phosphoenolpyruvate (PEP):carbohydrate phosphotransferase systems (PTSs) allocated for the uptake of glucose (PTSGlc), mannose (PTSMan), and fructose (PTSFru). PTS gene downregulation by c-di-GMP was alleviated in the absence of the three regulators, SgrS, Mlc, and Cra, suggesting their intermediary roles between c-di-GMP and PTS regulation. Moreover, Cra was found to bind to the promoters of ptsG, manX, and fruB. In contrast, c-di-GMP increased the transcription of genes important for gluconeogenesis. However, this effect of c-di-GMP in gluconeogenesis disappeared in the absence of Cra, indicating that Cra is a pivotal regulator that coordinates the carbon flux between PTS-mediated sugar uptake and gluconeogenesis, in response to cellular c-di-GMP concentrations. Since gluconeogenesis supplies precursor sugars required for extracellular polysaccharide production, Salmonella may exploit c-di-GMP as a dual-purpose signal that rewires carbon flux from glycolysis to gluconeogenesis and promotes biofilm formation using the end products of gluconeogenesis. This study sheds light on a new role for c-di-GMP in modulating carbon flux, to coordinate bacterial behavior in response to hostile environments. IMPORTANCE Cyclic di-GMP is a central signaling molecule that determines the transition between motile and nonmotile lifestyles in many bacteria. It stimulates biofilm formation at high concentrations but leads to biofilm dispersal and planktonic status at low concentrations. This study provides new insights into the role of c-di-GMP in programming carbon metabolic pathways. An increase in c-di-GMP downregulated the expression of PTS genes important for sugar uptake, while simultaneously upregulating the transcription of genes important for bacterial gluconeogenesis. The directly opposing effects of c-di-GMP on sugar metabolism were mediated by Cra (catabolite repressor/activator), a dual transcriptional regulator that modulates the direction of carbon flow. Salmonella may potentially harness c-di-GMP to promote its survival and fitness in hostile environments via the coordination of carbon metabolic pathways and the induction of biofilm formation.
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Affiliation(s)
- Jiwon Baek
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
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Li K, Chen L, Shi W, Hu C, Sha Y, Feng G, Wang E, Chen W, Sui X, Mi G. Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites. Environ Microbiol 2023; 25:473-492. [PMID: 36451600 DOI: 10.1111/1462-2920.16293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha-1 , LN) and high N (180 kg N ha-1 , HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N2 O emission and high rhizosphere NO3 - -N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.
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Affiliation(s)
- Keke Li
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - La Chen
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wenjun Shi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Conghui Hu
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Ye Sha
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guozhong Feng
- College of Resources and Environmental Science, Jilin Agricultural University, Changchun, China
- Key Laboratory of Soil Resource Sustainable Utilization for Jilin Province Commodity Grain Bases, Changchun, China
| | - Entao Wang
- Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional, Mexico City, Mexico
| | | | - Xinhua Sui
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Guohua Mi
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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103
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A Class IV Adenylate Cyclase, CyaB, Is Required for Capsule Polysaccharide Production and Biofilm Formation in Vibrio parahaemolyticus. Appl Environ Microbiol 2023; 89:e0187422. [PMID: 36602323 PMCID: PMC9888186 DOI: 10.1128/aem.01874-22] [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: 01/06/2023] Open
Abstract
Cyclic AMP (cAMP) receptor protein (CRP), encoded by crp, is a global regulator that is activated by cAMP, a second messenger synthesized by a class I adenylate cyclase (AC-I) encoded by cyaA in Escherichia coli. cAMP-CRP is required for growth on nonpreferred carbon sources and is a global regulator. We constructed in-frame nonpolar deletions of the crp and cyaA homologs in Vibrio parahaemolyticus and found that the Δcrp mutant did not grow in minimal media supplemented with nonpreferred carbon sources, but the ΔcyaA mutant grew similarly to the wild type. Bioinformatics analysis of the V. parahaemolyticus genome identified a 181-amino-acid protein annotated as a class IV adenylate cyclase (AC-IV) named CyaB, a member of the CYTH protein superfamily. AC-IV phylogeny showed that CyaB was present in Gammaproteobacteria and Alphaproteobacteria as well as Planctomycetes and Archaea. Only the bacterial CyaB proteins contained an N-terminal motif, HFxxxxExExK, indicative of adenylyl cyclase activity. Both V. parahaemolyticus cyaA and cyaB genes functionally complemented an E. coli ΔcyaA mutant. The Δcrp and ΔcyaB ΔcyaA mutants showed defects in growth on nonpreferred carbon sources and in swimming and swarming motility, indicating that cAMP-CRP is an activator. The ΔcyaA and ΔcyaB single mutants had no defects in these phenotypes, indicating that AC-IV complements AC-I. Capsule polysaccharide and biofilm production assays showed significant defects in the Δcrp, ΔcyaBΔcyaA, and ΔcyaB mutants, whereas the ΔcyaA strain behaved similarly to the wild type. This is consistent with a role of cAMP-CRP as an activator of these phenotypes and establishes a cellular role for AC-IV in capsule and biofilm formation, which to date has been unestablished. IMPORTANCE Here, we characterized the roles of CRP and CyaA in V. parahaemolyticus, showing that cAMP-CRP is an activator of metabolism, motility, capsule production, and biofilm formation. These results are in contrast to cAMP-CRP in V. cholerae, which represses capsule and biofilm formation. Previously, only an AC-I CyaA had been identified in Vibrio species. Our data showed that an AC-IV CyaB homolog is present in V. parahaemolyticus and is required for optimal growth. The data demonstrated that CyaB is essential for capsule production and biofilm formation, uncovering a physiological role of AC-IV in bacteria. The data showed that the cyaB gene was widespread among Vibrionaceae species and several other Gammaproteobacteria, but in general, its phylogenetic distribution was limited. Our phylogenetic analysis also demonstrated that in some species the cyaB gene was acquired by horizontal gene transfer.
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104
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Zeng L, Walker AR, Burne RA, Taylor ZA. Glucose Phosphotransferase System Modulates Pyruvate Metabolism, Bacterial Fitness, and Microbial Ecology in Oral Streptococci. J Bacteriol 2023; 205:e0035222. [PMID: 36468868 PMCID: PMC9879115 DOI: 10.1128/jb.00352-22] [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: 09/20/2022] [Accepted: 11/08/2022] [Indexed: 12/12/2022] Open
Abstract
Spontaneous mutants with defects in the primary glucose phosphotransferase permease (manLMNO) of Streptococcus sanguinis SK36 showed enhanced fitness at low pH. Transcriptomics and metabolomics with a manL deletion mutant (SK36/manL) revealed redirection of pyruvate to production of acetate and formate, rather than lactate. These observations were consistent with measurements of decreased lactic acid accumulation and increased excretion of acetate, formate, pyruvate, and H2O2. Genes showing increased expression in SK36/manL included those encoding carbohydrate transporters, extracellular glycosidases, intracellular polysaccharide metabolism, and arginine deiminase and pathways for metabolism of acetoin, ethanolamine, ascorbate, and formate, along with genes required for membrane biosynthesis and adhesion. Streptococcus mutans UA159 persisted much better in biofilm cocultures with SK36/manL than with SK36, an effect that was further enhanced by culturing the biofilms anaerobically but dampened by adding arginine to the medium. We posited that the enhanced persistence of S. mutans with SK36/manL was in part due to excess excretion of pyruvate by the latter, as addition of pyruvate to S. mutans-S. sanguinis cocultures increased the proportions of UA159 in the biofilms. Reducing the buffer capacity or increasing the concentration of glucose benefited UA159 when cocultured with SK36, but not with SK36/manL, likely due to the altered metabolism and enhanced acid tolerance of the mutant. When manL was deleted in S. mutans or Streptococcus gordonii, the mutants presented altered fitness characteristics. Our study demonstrated that phosphotransferase system (PTS)-dependent modulation of central metabolism can profoundly affect streptococcal fitness and metabolic interactions, revealing another dimension in commensal-pathogen relationships influencing dental caries development. IMPORTANCE Dental caries is underpinned by a dysbiotic microbiome and increased acid production. As beneficial bacteria that can antagonize oral pathobionts, oral streptococci such as S. sanguinis and S. gordonii can ferment many carbohydrates, despite their relative sensitivity to low pH. We characterized the molecular basis for why mutants of glucose transporter ManLMNO of S. sanguinis showed enhanced production of hydrogen peroxide and ammonia and improved persistence under acidic conditions. A metabolic shift involving more than 300 genes required for carbohydrate transport, energy production, and envelope biogenesis was observed. Significantly, manL mutants engineered in three different oral streptococci displayed altered capacities for acid production and interspecies antagonism, highlighting the potential for targeting the glucose-PTS to modulate the pathogenicity of oral biofilms.
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Affiliation(s)
- Lin Zeng
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Alejandro R. Walker
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Robert A. Burne
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Zachary A. Taylor
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
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105
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Barak-Gavish N, Dassa B, Kuhlisch C, Nussbaum I, Brandis A, Rosenberg G, Avraham R, Vardi A. Bacterial lifestyle switch in response to algal metabolites. eLife 2023; 12:e84400. [PMID: 36691727 PMCID: PMC9873259 DOI: 10.7554/elife.84400] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Unicellular algae, termed phytoplankton, greatly impact the marine environment by serving as the basis of marine food webs and by playing central roles in the biogeochemical cycling of elements. The interactions between phytoplankton and heterotrophic bacteria affect the fitness of both partners. It is becoming increasingly recognized that metabolic exchange determines the nature of such interactions, but the underlying molecular mechanisms remain underexplored. Here, we investigated the molecular and metabolic basis for the bacterial lifestyle switch, from coexistence to pathogenicity, in Sulfitobacter D7 during its interaction with Emiliania huxleyi, a cosmopolitan bloom-forming phytoplankter. To unravel the bacterial lifestyle switch, we analyzed bacterial transcriptomes in response to exudates derived from algae in exponential growth and stationary phase, which supported the Sulfitobacter D7 coexistence and pathogenicity lifestyles, respectively. In pathogenic mode, Sulfitobacter D7 upregulated flagellar motility and diverse transport systems, presumably to maximize assimilation of E. huxleyi-derived metabolites released by algal cells upon cell death. Algal dimethylsulfoniopropionate (DMSP) was a pivotal signaling molecule that mediated the transition between the lifestyles, supporting our previous findings. However, the coexisting and pathogenic lifestyles were evident only in the presence of additional algal metabolites. Specifically, we discovered that algae-produced benzoate promoted the growth of Sulfitobacter D7 and hindered the DMSP-induced lifestyle switch to pathogenicity, demonstrating that benzoate is important for maintaining the coexistence of algae and bacteria. We propose that bacteria can sense the physiological state of the algal host through changes in the metabolic composition, which will determine the bacterial lifestyle during interaction.
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Affiliation(s)
- Noa Barak-Gavish
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Bareket Dassa
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Constanze Kuhlisch
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Inbal Nussbaum
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
| | - Alexander Brandis
- Life Sciences Core Facilities, Weizmann Institute of ScienceRehovotIsrael
| | - Gili Rosenberg
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Roi Avraham
- Department of Biological Regulation, Weizmann Institute of ScienceRehovotIsrael
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of ScienceRehovotIsrael
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106
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Proline transporters ProT and PutP are required for Staphylococcus aureus infection. PLoS Pathog 2023; 19:e1011098. [PMID: 36652494 PMCID: PMC9886301 DOI: 10.1371/journal.ppat.1011098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/30/2023] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Proline acquired via specific transporters can serve as a proteinogenic substrate, carbon and nitrogen source, or osmolyte. Previous reports have documented that Staphylococcus aureus, a major community and nosocomial pathogen, encodes at least four proline transporters, PutP, OpuC, OpuD, and ProP. A combination of genetic approaches and 3H-proline transport assays reveal that a previously unrecognized transporter, ProT, in addition to PutP, are the major proline transporters in S. aureus. Complementation experiments using constitutively expressed non-cognate promoters found that proline transport via OpuD, OpuC, and ProP is minimal. Both proline biosynthesis from arginine and proline transport via ProT are critical for growth when S. aureus is grown under conditions of high salinity. Further, proline transport mediated by ProT or PutP are required for growth in media with and without glucose, indicating both transporters function to acquire proline for proteinogenic purposes in addition to acquisition of proline as a carbon/nitrogen source. Lastly, inactivation of proT and putP resulted in a significant reduction (5 log10) of bacterial burden in murine skin-and-soft tissue infection and bacteremia models, suggesting that proline transport is required to establish a S. aureus infection.
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107
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Costa MDOCE, do Nascimento APB, Martins YC, dos Santos MT, Figueiredo AMDS, Perez-Rueda E, Nicolás MF. The gene regulatory network of Staphylococcus aureus ST239-SCC mecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds. Front Microbiol 2023; 13:1049819. [PMID: 36704545 PMCID: PMC9871828 DOI: 10.3389/fmicb.2022.1049819] [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: 09/21/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction Staphylococcus aureus is one of the most prevalent and relevant pathogens responsible for a wide spectrum of hospital-associated or community-acquired infections. In addition, methicillin-resistant Staphylococcus aureus may display multidrug resistance profiles that complicate treatment and increase the mortality rate. The ability to produce biofilm, particularly in device-associated infections, promotes chronic and potentially more severe infections originating from the primary site. Understanding the complex mechanisms involved in planktonic and biofilm growth is critical to identifying regulatory connections and ways to overcome the global health problem of multidrug-resistant bacteria. Methods In this work, we apply literature-based and comparative genomics approaches to reconstruct the gene regulatory network of the high biofilm-producing strain Bmb9393, belonging to one of the highly disseminating successful clones, the Brazilian epidemic clone. To the best of our knowledge, we describe for the first time the topological properties and network motifs for the Staphylococcus aureus pathogen. We performed this analysis using the ST239-SCCmecIII Bmb9393 strain. In addition, we analyzed transcriptomes available in the literature to construct a set of genes differentially expressed in the biofilm, covering different stages of the biofilms and genetic backgrounds of the strains. Results and discussion The Bmb9393 gene regulatory network comprises 1,803 regulatory interactions between 64 transcription factors and the non-redundant set of 1,151 target genes with the inclusion of 19 new regulons compared to the N315 transcriptional regulatory network published in 2011. In the Bmb9393 network, we found 54 feed-forward loop motifs, where the most prevalent were coherent type 2 and incoherent type 2. The non-redundant set of differentially expressed genes in the biofilm consisted of 1,794 genes with functional categories relevant for adaptation to the variable microenvironments established throughout the biofilm formation process. Finally, we mapped the set of genes with altered expression in the biofilm in the Bmb9393 gene regulatory network to depict how different growth modes can alter the regulatory systems. The data revealed 45 transcription factors and 876 shared target genes. Thus, the gene regulatory network model provided represents the most up-to-date model for Staphylococcus aureus, and the set of genes altered in the biofilm provides a global view of their influence on biofilm formation from distinct experimental perspectives and different strain backgrounds.
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Affiliation(s)
| | - Ana Paula Barbosa do Nascimento
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | | | | | - Agnes Marie de Sá Figueiredo
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Merida, Mexico
| | - Ernesto Perez-Rueda
- Laboratório de Biologia Molecular de Bactérias, Instituto de Microbiologia Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil,*Correspondence: Ernesto Perez-Rueda ✉
| | - Marisa Fabiana Nicolás
- Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil,Marisa Fabiana Nicolás ✉
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108
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Esteban-Torres M, Ruiz L, Rossini V, Nally K, van Sinderen D. Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait. Gut Microbes 2023; 15:2235067. [PMID: 37526383 PMCID: PMC10395257 DOI: 10.1080/19490976.2023.2235067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.
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Affiliation(s)
- Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, IPLA-CSIC, Villaviciosa, Spain
- Functionality and Ecology of Benefitial Microbes (MicroHealth Group), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Valerio Rossini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ken Nally
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
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109
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Suo W, Guo X, Zhang X, Xiao S, Wang S, Yin Y, Zheng Y. Glucose levels affect MgaSpn regulation on the virulence and adaptability of Streptococcus pneumoniae. Microb Pathog 2023; 174:105896. [PMID: 36460142 DOI: 10.1016/j.micpath.2022.105896] [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: 09/20/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
Streptococcus pneumoniae can regulate virulence gene expression by sensing environmental changes, which is key to its pathogenicity. The global transcription regulator MgaSpn of Streptococcus pneumoniae regulates virulence genes expression by directly binding to the promoter regions, but its role in response to different environments remains unclear. In this study, we found that glucose levels could affect phosphocholine content, which was mediated by MgaSpn. MgaSpn can also alter its anti-phagocytosis ability, depending on the availability of glucose. In addition, transcriptome analysis of wild-type D39s in low and high glucose concentrations revealed that MgaSpn was also involved in the regulation of carbon metabolism inhibition (carbon catabolite repression; CCR) and translation processes, which made S. pneumoniae highly competitive in fluctuating environments. In conclusion, MgaSpn is closely related to the virulence and environmental adaptability of Streptococcus pneumoniae.
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Affiliation(s)
- Weicai Suo
- Department of Medicine Laboratory, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, and Chongqing Key Laboratory of Pediatrics, Chongqing, PR China
| | - Xinlin Guo
- Department of Medicine Laboratory, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, and Chongqing Key Laboratory of Pediatrics, Chongqing, PR China
| | - Xuemei Zhang
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Chongqing Medical University, Chongqing, PR China
| | - Shengnan Xiao
- Precision Medicine Center, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China
| | - Shuhui Wang
- Department of Medicine Laboratory, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, and Chongqing Key Laboratory of Pediatrics, Chongqing, PR China
| | - Yibing Yin
- Key Laboratory of Diagnostic Medicine Designated by the Ministry of Education, Chongqing Medical University, Chongqing, PR China
| | - Yuqiang Zheng
- Department of Medicine Laboratory, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, and Chongqing Key Laboratory of Pediatrics, Chongqing, PR China.
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110
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Moreno R, Rojo F. The importance of understanding the regulation of bacterial metabolism. Environ Microbiol 2023; 25:54-58. [PMID: 35859345 PMCID: PMC10084369 DOI: 10.1111/1462-2920.16123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Renata Moreno
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Fernando Rojo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
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Suyama T, Kanno N, Matsukura S, Chihara K, Noda N, Hanada S. Transcriptome and Deletion Mutant Analyses Revealed that an RpoH Family Sigma Factor Is Essential for Photosystem Production in Roseateles depolymerans under Carbon Starvation. Microbes Environ 2023; 38. [PMID: 36878600 PMCID: PMC10037100 DOI: 10.1264/jsme2.me22072] [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] [Indexed: 03/08/2023] Open
Abstract
Roseateles depolymerans is an obligately aerobic bacterium that produces a photosynthetic apparatus only under the scarcity of carbon substrates. We herein examined changes in the transcriptomes of R. depolymerans cells to clarify the expression of photosynthesis genes and their upstream regulatory factors under carbon starvation. Transcriptomes 0, 1, and 6 h after the depletion of a carbon substrate indicated that transcripts showing the greatest variations (a 500-fold increase [6 h/0 h]) were light-harvesting proteins (PufA and PufB). Moreover, loci with more than 50-fold increases (6 h/0 h) were fully related to the photosynthetic gene cluster. Among 13 sigma factor genes, the transcripts of a sigma 70 family sigma factor related to RpoH (SP70) increased along photosynthesis genes under starvation; therefore, a knockout experiment of SP70 was performed. ΔSP70 mutants were found to lack photosynthetic pigments (carotenoids and bacteriochlo-rophyll a) regardless of carbon starvation. We also examined the effects of heat stress on ΔSP70 mutants, and found that SP70 was also related to heat stress tolerance, similar to other RpoH sigma factors (while heat stress did not trigger photosystem production). The deficient accumulation of photosynthetic pigments and the heat stress tolerance of ΔSP70 mutants were both complemented by the introduction of an intact SP70 gene. Furthermore, the transcription of photosynthetic gene operons (puf, puh, and bch) was markedly reduced in the ΔSP70 mutant. The RpoH homologue SP70 was concluded to be a sigma factor that is essential for the transcription of photosynthetic gene operons in R. depolymerans.
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Affiliation(s)
- Tetsushi Suyama
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Nanako Kanno
- Photosynthetic Microbial Consortia Laboratory, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
| | - Satoko Matsukura
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Kotaro Chihara
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Department of Life Science and Medical Bioscience, Waseda University
| | - Naohiro Noda
- Bio-Analytical Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Department of Life Science and Medical Bioscience, Waseda University
| | - Satoshi Hanada
- Photosynthetic Microbial Consortia Laboratory, Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University
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Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models. mSystems 2022; 7:e0090022. [PMID: 36409084 PMCID: PMC9765429 DOI: 10.1128/msystems.00900-22] [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] [Indexed: 11/23/2022] Open
Abstract
Attempts to understand gene regulation by global transcription factors have largely been limited to expression studies under binary conditions of presence and absence of the transcription factor. Studies addressing genome-wide transcriptional responses to changing transcription factor concentration at high resolution are lacking. Here, we create a data set containing the entire Escherichia coli transcriptome in Luria-Bertani (LB) broth as it responds to 10 different cAMP concentrations spanning the biological range. We use the Hill's model to accurately summarize individual gene responses into three intuitively understandable parameters, Emax, n, and k, reflecting the sensitivity, nonlinearity, and midpoint of the dynamic range. Our data show that most cAMP-regulated genes have an n of >2, with their k values centered around the wild-type concentration of cAMP. Additionally, cAMP receptor protein (CRP) affinity to a promoter is correlated with Emax but not k, hinting that a high-affinity CRP promoter need not ensure transcriptional activation at lower cAMP concentrations and instead affects the magnitude of the response. Finally, genes belonging to different functional classes are tuned to have different k, n, and Emax values. We demonstrate that phenomenological models are a better alternative for studying gene expression trends than classical clustering methods, with the phenomenological constants providing greater insights into how genes are tuned in a regulatory network. IMPORTANCE Different genes may follow different trends in response to various transcription factor concentrations. In this study, we ask two questions: (i) what are the trends that different genes follow in response to changing transcription factor concentrations and (ii) what methods can be used to extract information from the gene trends so obtained. We demonstrate a method to analyze transcription factor concentration-dependent genome-wide expression data using phenomenological models. Conventional clustering methods and principal-component analysis (PCA) can be used to summarize trends in data but have limited interpretability. The use of phenomenological models greatly enhances the interpretability and thus utility of conventional clustering. Transformation of dose-response data into phenomenological constants opens up avenues to ask and answer many different kinds of question. We show that the phenomenological constants obtained from the model fits can be used to generate insights about network topology and allows integration of other experimental data such as chromatin immunoprecipitation sequencing (ChIP-seq) to understand the system in greater detail.
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Pareek M, Hegedüs B, Hou Z, Csernetics Á, Wu H, Virágh M, Sahu N, Liu XB, Nagy L. Preassembled Cas9 Ribonucleoprotein-Mediated Gene Deletion Identifies the Carbon Catabolite Repressor and Its Target Genes in Coprinopsis cinerea. Appl Environ Microbiol 2022; 88:e0094022. [PMID: 36374019 PMCID: PMC9746306 DOI: 10.1128/aem.00940-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. The cre1 gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota species remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. We used a rapid and efficient gene deletion approach based on PCR-amplified split-marker DNA cassettes together with in vitro assembled Cas9-guide RNA ribonucleoproteins (Cas9 RNPs) to generate C. cinerea cre1 gene deletion strains. Gene expression profiling of two independent C. cinerea cre1 mutants showed significant deregulation of carbohydrate metabolism, plant cell wall degrading enzymes (PCWDEs), plasma membrane transporter-related and several transcription factor-encoding genes, among others. Our results support the notion that, like reports in the ascomycetes, Cre1 of C. cinerea orchestrates CCR through a combined regulation of diverse genes, including PCWDEs, transcription factors that positively regulate PCWDEs, and membrane transporters which could import simple sugars that can induce the expression of PWCDEs. Somewhat paradoxically, though in accordance with other Agaricomycetes, genes related to lignin degradation were mostly downregulated in cre1 mutants, indicating they fall under different regulation than other PCWDEs. The gene deletion approach and the data presented here will expand our knowledge of CCR in the Basidiomycota and provide functional hypotheses on genes related to plant biomass degradation. IMPORTANCE Mushroom-forming fungi include some of the most efficient lignocellulosic plant biomass degraders. They degrade dead plant materials by a battery of lignin-, cellulose-, hemicellulose-, and pectin-degrading enzymes, the encoding genes of which are under tight transcriptional control. One of the highest-level regulations of these metabolic enzymes is known as carbon catabolite repression, which is orchestrated by the transcription factor Cre1, and ensures that costly lignocellulose-degrading enzyme genes are expressed only when simple carbon sources (e.g., glucose) are not available. Here, we identified the Cre1 ortholog in a litter decomposer Agaricomycete, Coprinopsis cinerea, knocked it out, and characterized transcriptional changes in the mutants. We identified several dozen lignocellulolytic enzyme genes as well as membrane transporters and other transcription factors as putative target genes of C. cinerea cre1. These results extend knowledge on carbon catabolite repression to litter decomposer Basidiomycota.
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Affiliation(s)
- Manish Pareek
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Botond Hegedüs
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Zhihao Hou
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Árpád Csernetics
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Hongli Wu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Máté Virágh
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Neha Sahu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - László Nagy
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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114
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Zhang C, Cheng H, Han Y, Wa Y, Chen D, Guan C, Huang Y, Gu R. Transcriptome-phenotype matching analysis of how nitrogen sources influence Lacticaseibacillus rhamnosus tolerance to heat stress and oxidative stress. Microb Cell Fact 2022; 21:257. [PMID: 36510221 PMCID: PMC9746023 DOI: 10.1186/s12934-022-01985-0] [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: 11/18/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Spray drying is the most cost-effective production method for lactic acid bacteria starters, but heat and oxidative stresses result in low survival rates. The heat stress and oxidative stress tolerance of Lacticaseibacillus rhamnosus cultured in tryptone-free MRS (NP-MRS) broth was much stronger than that in MRS or tryptone-free MRS broth supplemented with phenylalanine (Phe-MRS). Here, multiple transcriptome-phenotype matching was performed on cells cultured in NP-MRS, MRS and Phe-MRS broths to reveal the mechanism by which nitrogen sources influence L. rhamnosus tolerance to heat stress and oxidative stress. RESULTS Compared with cells cultured in NP-MRS broth, 83 overlapping differentially expressed genes (DEGs) were downregulated by either tryptone or phenylalanine. The overlapping DEGs were mainly classified into carbohydrate metabolism and membrane transport pathways, which are often repressed by glucose during carbon catabolite repression (CCR). In the presence of glucose, the heat stress or oxidative stress tolerance of L. rhamnosus hsryfm 1301 was not strengthened by supplementation with secondary carbohydrates. Replacing glucose with mannose, fructose or ribose improved the heat stress and oxidative stress tolerance of L. rhamnosus hsryfm 1301 (5 to 46-fold). CONCLUSIONS Alleviation of CCR might be a reason for the resistance of L. rhamnosus hsryfm 1301 to heat stress and oxidative stress in a low-nitrogen environment. The survival rate of L. rhamnosus during spray drying will hopefully be improved by relieving CCR. It is a new discovery that nitrogen sources influence CCR in L. rhamnosus.
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Affiliation(s)
- Chenchen Zhang
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China.,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China.,Jiangsu Dairy Biotechnology Engineering Research Center, Yangzhou, People's Republic of China
| | - Haohao Cheng
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China.,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China
| | - Yuemei Han
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China.,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China
| | - Yunchao Wa
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China.,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China
| | - Dawei Chen
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China.,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China
| | - Chengran Guan
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China.,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China.,Jiangsu Dairy Biotechnology Engineering Research Center, Yangzhou, People's Republic of China
| | - Yujun Huang
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China.,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China
| | - Ruixia Gu
- College of Food Science and Engineering, Yangzhou University, 196 Huayang Xilu, Yangzhou, 225100, People's Republic of China. .,Jiangsu Key Laboratory of Dairy Biotechnology and Safety Control, Yangzhou, People's Republic of China.
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115
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Woo S, Moon JH, Sung J, Baek D, Shon YJ, Jung GY. Recent Advances in the Utilization of Brown Macroalgae as Feedstock for Microbial Biorefinery. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0301-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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116
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Zhong X, Ma J, Bai Q, Zhu Y, Zhang Y, Gu Q, Pan Z, Liu G, Wu Z, Yao H. Identification of the RNA-binding domain-containing protein RbpA that acts as a global regulator of the pathogenicity of Streptococcus suis serotype 2. Virulence 2022; 13:1304-1314. [PMID: 35903019 PMCID: PMC9341378 DOI: 10.1080/21505594.2022.2103233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Streptococcus suis serotype 2 (SS2), an emerging zoonotic pathogen, causes swine diseases and human cases of streptococcal toxic shock syndrome. RNA-binding proteins (RBPs) can modulate gene expression through post-transcriptional regulation. In this study, we identified an RBP harbouring an S1 domain, named RbpA, which facilitated SS2 adhesion to host epithelial cells and contributed to bacterial pathogenicity. Comparative proteomic analysis identified 145 proteins that were expressed differentially between ΔrbpA strain and wild-type strain, including several virulence-associated factors, such as the extracellular protein factor (EF), SrtF pilus, IgA1 protease, SBP2 pilus, and peptidoglycan-binding LysM’ proteins. The mechanisms underlying the regulatory effects of RbpA on their encoding genes were explored, and it was found that RbpA regulates gene expression through diverse mechanisms, including post-transcriptional regulation, and thus acts as a global regulator. These results partly reveal the pathogenic mechanism mediated by RbpA, improving our understanding of the regulatory systems of S. suis and providing new insights into bacterial pathogenicity.
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Affiliation(s)
- Xiaojun Zhong
- College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Jiale Ma
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qiankun Bai
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Yinchu Zhu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yue Zhang
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qibing Gu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zihao Pan
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Guangjin Liu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zongfu Wu
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Huochun Yao
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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117
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Mahilkar A, Nagendra P, Alugoju P, E R, Saini S. Public good-driven release of heterogeneous resources leads to genotypic diversification of an isogenic yeast population. Evolution 2022; 76:2811-2828. [PMID: 36181481 PMCID: PMC7614384 DOI: 10.1111/evo.14646] [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: 04/24/2022] [Accepted: 09/22/2022] [Indexed: 01/22/2023]
Abstract
Understanding the basis of biological diversity remains a central problem in evolutionary biology. Using microbial systems, adaptive diversification has been studied in (a) spatially heterogeneous environments, (b) temporally segregated resources, and (c) resource specialization in a homogeneous environment. However, it is not well understood how adaptive diversification can take place in a homogeneous environment containing a single resource. Starting from an isogenic population of yeast Saccharomyces cerevisiae, we report rapid adaptive diversification, when propagated in an environment containing melibiose as the carbon source. The diversification is driven due to a public good enzyme α-galactosidase, which hydrolyzes melibiose into glucose and galactose. The diversification is driven by mutations at a single locus, in the GAL3 gene in the S. cerevisiae GAL/MEL regulon. We show that metabolic co-operation involving public resources could be an important mode of generating biological diversity. Our study demonstrates sympatric diversification of yeast starting from an isogenic population and provides detailed mechanistic insights into the factors and conditions responsible for generating and maintaining the population diversity.
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Affiliation(s)
- Anjali Mahilkar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Prachitha Nagendra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Phaniendra Alugoju
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Rajeshkannan E
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Supreet Saini
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
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118
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Sugiura H, Fukunishi K, Kawakami H, Imajoh M. Phenotypic differences between Edwardsiella piscicida and Edwardsiella anguillarum isolates in Japan. JOURNAL OF AQUATIC ANIMAL HEALTH 2022; 34:197-207. [PMID: 35959541 DOI: 10.1002/aah.10169] [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: 05/16/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE Edwardsiella tarda has been regarded as the causative agent of edwardsiellosis in cultured marine and freshwater fish species in Japan. Our previous study genetically classified an E. tarda-like isolate from diseased Olive Flounder Paralichthys olivaceus as E. piscicida and that from diseased Red Seabream Pagrus major as E. anguillarum. This study aimed to understand the phenotypic differences between E. piscicida and E. anguillarum. METHODS Fourteen E. piscicida and seven E. anguillarum isolates were used in this study. The colonies of each isolate were grown on brain-heart infusion agar plates and then subjected to DNA extraction. The extracted DNA was amplified using PCR. carbohydrate fermentation of the isolates was examined using API 50 CH test kits. Moreover, the growth of the two species was examined in defined media. Also, free amino acids in Olive Flounder and Red Seabream sera were detected and quantified via high-performance liquid chromatography-mass spectrometry. Statistical differences in the concentrations of free amino acids were analyzed using Welch's t-tests. RESULT The API 50 CH test revealed that L-arabinose and D-mannitol were fermented by E. anguillarum isolates but not E. piscicida isolates. Furthermore, the growth of E. piscicida and E. anguillarum was reduced in the defined medium without methionine and iron sulfate. The growth of E. piscicida was reduced in the defined medium without phenylalanine, tyrosine, alanine, or nicotinic acid, whereas the growth of E. anguillarum was reduced in the defined medium without serine, cysteine, leucine, threonine, or isoleucine. Tyrosine and alanine were present in higher concentrations in the Olive Flounder serum, whereas threonine and isoleucine were present in higher concentrations in the Red Seabream serum, suggesting favorable growth conditions for E. piscicida and E. anguillarum. CONCLUSION This study characterizes a minimal defined medium that can be used for developing vaccines against E. piscicida and E. anguillarum.
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Affiliation(s)
- Hidehiro Sugiura
- Department of Bioresource Production Science, The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan
| | - Kosuke Fukunishi
- Graduate School of Integrated Arts and Science, Kochi University, Nankoku, Japan
| | | | - Masayuki Imajoh
- Department of Bioresource Production Science, The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Japan
- Laboratory of Fish Disease, Aquaculture Course, Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan
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119
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Gevorgyan H, Khalatyan S, Vassilian A, Trchounian K. Metabolic pathways and ΔpH regulation in Escherichia coli during the fermentation of glucose and glycerol in the presence of formate at pH 6.5: the role of FhlA transcriptional activator. FEMS Microbiol Lett 2022; 369:6825452. [PMID: 36370455 DOI: 10.1093/femsle/fnac109] [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: 03/23/2022] [Revised: 10/08/2022] [Accepted: 11/10/2022] [Indexed: 11/14/2022] Open
Abstract
Escherichia coli is able to ferment mixed carbon sources and produce various fermentation end-products. In this study, the function of FhlA protein in the specific growth rate (µ), metabolism, regulation of ΔpH and proton ATPase activity was investigated. Reduced µ in fhlA mutant of ∼25% was shown, suggesting the role of FhlA in the growth process. The utilization rate of glycerol is decreased in fhlA ∼ 2 fold, depending on the oxidation-reduction potential values. Bacteria regulate the activity of hydrogenase enzymes during growth depending on the external pH, which manifests as a lack of hydrogen gas generation during glycerol utilization at pH values below 5.9. It is suggested that cells maintain ΔpH during the fermentative growth via formate-lactate-succinate exchange. The decrement of the value of pHin, but not of pHex in mutant cells, is regulating ΔpH and consequently proton motive force generation.
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Affiliation(s)
- Heghine Gevorgyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Satenik Khalatyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
| | - Anait Vassilian
- Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia
| | - Karen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Scientific-Research Institute of Biology, Faculty of Biology, Yerevan State University, 0025 Yerevan, Armenia.,Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025 Yerevan, Armenia
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120
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Lv F, Zhan Y, Lu W, Ke X, Shao Y, Ma Y, Zheng J, Yang Z, Jiang S, Shang L, Ma Y, Cheng L, Elmerich C, Yan Y, Lin M. Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri. iScience 2022; 25:105663. [PMID: 36505936 PMCID: PMC9730152 DOI: 10.1016/j.isci.2022.105663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse order to that of enterobacteria, and this process is controlled by RNA-binding translational repressors and regulatory ncRNA antagonists. However, their roles in microbe-plant interactions and the underlying mechanisms remain uncertain. Here we show that root-associated diazotrophic Pseudomonas stutzeri A1501 preferentially catabolizes succinate, followed by the less favorable substrate citrate, and ultimately glucose. Furthermore, the Hfq/Crc/CrcZY regulatory system orchestrates this preference and contributes to optimal nitrogenase activity and efficient root colonization. Hfq has a central role in this regulatory network through different mechanisms of action, including repressing the translation of substrate-specific catabolic genes, activating the nitrogenase gene nifH posttranscriptionally, and exerting a positive effect on the transcription of an exopolysaccharide gene cluster. Our results illustrate an Hfq-mediated mechanism linking carbon metabolism to nitrogen fixation and root colonization, which may confer rhizobacteria competitive advantages in rhizosphere environments.
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Affiliation(s)
- Fanyang Lv
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua Zhan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Lu
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiubin Ke
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yahui Shao
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yiyuan Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Zheng
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhimin Yang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shanshan Jiang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liguo Shang
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yao Ma
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | | | - Yongliang Yan
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Corresponding author
| | - Min Lin
- Biotechnology Research Institute/Key Laboratory of Agricultural Microbiome (MARA), Chinese Academy of Agricultural Sciences, Beijing, China,Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China,Corresponding author
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121
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Baleeiro FCF, Raab J, Kleinsteuber S, Neumann A, Sträuber H. Mixotrophic chain elongation with syngas and lactate as electron donors. Microb Biotechnol 2022; 16:322-336. [PMID: 36378491 PMCID: PMC9871530 DOI: 10.1111/1751-7915.14163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Feeding microbial communities with both organic and inorganic substrates can improve sustainability and feasibility of chain elongation processes. Sustainably produced H2 , CO2 , and CO can be co-fed to microorganisms as a source for acetyl-CoA, while a small amount of an ATP-generating organic substrate helps overcome the kinetic hindrances associated with autotrophic carboxylate production. Here, we operated two semi-continuous bioreactor systems with continuous recirculation of H2 , CO2 , and CO while co-feeding an organic model feedstock (lactate and acetate) to understand how a mixotrophic community is shaped during carboxylate production. Contrary to the assumption that H2 , CO2 , and CO support chain elongation via ethanol production in open cultures, significant correlations (p < 0.01) indicated that relatives of Clostridium luticellarii and Eubacterium aggregans produced carboxylates (acetate to n-caproate) while consuming H2 , CO2 , CO, and lactate themselves. After 100 days, the enriched community was dominated by these two bacteria coexisting in cyclic dynamics shaped by the CO partial pressure. Homoacetogenesis was strongest when the acetate concentration was low (3.2 g L-1 ), while heterotrophs had the following roles: Pseudoramibacter, Oscillibacter, and Colidextribacter contributed to n-caproate production and Clostridium tyrobutyricum and Acidipropionibacterium spp. grew opportunistically producing n-butyrate and propionate, respectively. The mixotrophic chain elongation community was more efficient in carboxylate production compared with the heterotrophic one and maintained average carbon fixation rates between 0.088 and 1.4 g CO2 equivalents L-1 days-1 . The extra H2 and CO consumed routed 82% more electrons to carboxylates and 50% more electrons to carboxylates longer than acetate. This study shows for the first time long-term, stable production of short- and medium-chain carboxylates with a mixotrophic community.
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Affiliation(s)
- Flávio C. F. Baleeiro
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany,Technical Biology, Institute of Process Engineering in Life ScienceKarlsruhe Institute of Technology – KITKarlsruheGermany
| | - Jana Raab
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Sabine Kleinsteuber
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
| | - Anke Neumann
- Technical Biology, Institute of Process Engineering in Life ScienceKarlsruhe Institute of Technology – KITKarlsruheGermany
| | - Heike Sträuber
- Department of Environmental MicrobiologyHelmholtz Centre for Environmental Research – UFZLeipzigGermany
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Tan MF, Tan J, Zhang FF, Li HQ, Ji HY, Fang SP, Wu CC, Rao YL, Zeng YB, Yang Q. Exogenous glycogen utilization effects the transcriptome and pathogenicity of Streptococcus suis serotype 2. Front Cell Infect Microbiol 2022; 12:938286. [DOI: 10.3389/fcimb.2022.938286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 10/24/2022] [Indexed: 11/10/2022] Open
Abstract
Streptococcus suis serotype 2 (SS2) is an important zoonotic pathogen that causes severe infections in humans and the swine industry. Acquisition and utilization of available carbon sources from challenging host environments is necessary for bacterial pathogens to ensure growth and proliferation. Glycogen is abundant in mammalian body and may support the growth of SS2 during infection in hosts. However, limited information is known about the mechanism between the glycogen utilization and host adaptation of SS2. Here, the pleiotropic effects of exogenous glycogen on SS2 were investigated through transcriptome sequencing. Analysis of transcriptome data showed that the main basic metabolic pathways, especially the core carbon metabolism pathways and virulence-associated factors, of SS2 responded actively to glycogen induction. Glycogen induction led to the perturbation of the glycolysis pathway and citrate cycle, but promoted the pentose phosphate pathway and carbohydrate transport systems. Extracellular glycogen utilization also promoted the mixed-acid fermentation in SS2 rather than homolactic fermentation. Subsequently, apuA, a gene encoding the unique bifunctional amylopullulanase for glycogen degradation, was deleted from the wild type and generated the mutant strain ΔapuA. The pathogenicity details of the wild type and ΔapuA cultured in glucose and glycogen were investigated and compared. Results revealed that the capsule synthesis or bacterial morphology were not affected by glycogen incubation or apuA deletion. However, extracellular glycogen utilization significantly enhanced the hemolytic activity, adhesion and invasion ability, and lethality of SS2. The deletion of apuA also impaired the pathogenicity of bacteria cultured in glucose, indicating that ApuA is indeed an important virulence factor. Our results revealed that exogenous glycogen utilization extensively influenced the expression profile of the S. suis genome. Based on the transcriptome response, exogenous glycogen utilization promoted the carbon adaption and pathogenicity of SS2.
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Bell E, Rattray JE, Sloan K, Sherry A, Pilloni G, Hubert CRJ. Hyperthermophilic endospores germinate and metabolize organic carbon in sediments heated to 80°C. Environ Microbiol 2022; 24:5534-5545. [PMID: 36100999 PMCID: PMC9826295 DOI: 10.1111/1462-2920.16167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 08/10/2022] [Indexed: 01/11/2023]
Abstract
Cold surface sediments host a seedbank of functionally diverse thermophilic bacteria. These thermophiles are present as endospores, which are widely dispersed in aquatic environments. Here, we investigated the functional potential of endospore populations in cold surface sediments heated to 80°C. Microbial production of acetate was observed at 80°C and could be enhanced by supplying additional organic carbon substrates. Comparison of 16S rRNA gene amplicon libraries from 80°C enrichments to sediments heated to lower temperatures (50-70°C) showed that temperature selects for distinct populations of endospore-forming bacteria. Whereas sulfate-reducing thermophiles were enriched in 50-70°C incubations, 80°C exceeds their thermal tolerance and selects for hyperthermophilic organotrophic bacteria that are similarly detected in amplicon libraries from sediments heated to 90°C. Genome-resolved metagenomics revealed novel carbon cycling members of Symbiobacteriales, Thermosediminibacteraceae, Thermanaeromonas and Calditerricola with the genomic potential for the degradation of carbohydrates, sugars, amino acids and nucleotides. Endospores of thermophilic bacteria are deposited on seabed sediments worldwide where they remain dormant as they are buried in the accumulating sediments. Our results suggest that endospore populations could be activated by temperature increases encountered during burial and show the potential for organotrophic metabolic activity contributing to acetate generation in deep hot sediments.
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Affiliation(s)
- Emma Bell
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada,School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Jayne E. Rattray
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Kathryn Sloan
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Angela Sherry
- Hub for Biotechnology in the Built Environment, Department of Applied SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Giovanni Pilloni
- ExxonMobil Technology and Engineering CompanyAnnandaleNew JerseyUSA
| | - Casey R. J. Hubert
- Geomicrobiology Group, Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada,School of Natural and Environmental SciencesNewcastle UniversityNewcastle upon TyneUK
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Derix J, Ducatelle R, Pardon B, Croes E, Nibbelink NG, Van Deurzen-Duineveld L, Van Immerseel F, Goossens E. The in vitro effect of lactose on Clostridium perfringens alpha toxin production and the implications of lactose consumption for in vivo anti-alpha toxin antibody production. J Dairy Sci 2022; 106:733-742. [DOI: 10.3168/jds.2022-22467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022]
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Han X, Liu J, Tian S, Tao F, Xu P. Microbial cell factories for bio-based biodegradable plastics production. iScience 2022; 25:105462. [DOI: 10.1016/j.isci.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Pn-AqpC-Mediated Fermentation Pattern Coordination with the Two-Component System 07 Regulates Host N-Glycan Degradation of Streptococcus pneumoniae. Microbiol Spectr 2022; 10:e0249622. [PMID: 36106896 PMCID: PMC9603416 DOI: 10.1128/spectrum.02496-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The opportunistic pathogen Streptococcus pneumoniae (pneumococcus) is a human nasopharyngeal commensal, and host N-glycan metabolism promotes its colonization and invasion. It has been reported that glucose represses, while fetuin, a glycoconjugated model protein, induces, the genes involved in N-glycan degradation through the two-component system TCS07. However, the mechanisms of glucose repression and TCS07 induction remain unknown. Previously, we found that the pneumococcal aquaglyceroporin Pn-AqpC facilitates oxygen uptake, thereby contributing to the antioxidant potential and virulence. In this study, through Tandem Mass Tag (TMT) quantitative proteomics, we found that the deletion of Pn-aqpC caused a marked upregulation of 11 proteins involved in N-glycan degradation in glucose-grown pneumococcus R6. Both quantitative RT-PCR and GFP fluorescence reporters revealed that the upregulation of N-glycan genes was completely dependent on response regulator (RR) 07, but not on the histidine kinase HK07 of TCS07 or the phosphoryl-receiving aspartate residue of RR07 in ΔPn-aqpC, indicating that RR07 was activated in an HK07-independent manner when Pn-AqpC was absent. The deletion of Pn-aqpC also enhanced the expression of pyruvate formate lyase and increased formate production, probably due to reduced cellular oxygen content, indicating that a shunt of glucose catabolism to mixed acid fermentation occurs. Notably, formate induced the N-glycan degradation genes in glucose-grown R6, but the deletion of rr07 abolished this induction, indicating that formate activates RR07. However, the induction of N-glycan degradation proteins reduced the intraspecies competition of R6 in glucose. Therefore, although N-glycan degradation promotes pneumococcal pathogenesis, the glucose metabolites-based RR07 regulation reported here is of importance for balancing growth fitness and the pathogenicity of pneumococcus. IMPORTANCE Pneumococcus, a human opportunistic pathogen, is capable of metabolizing host complex N-glycans. N-glycan degradation promotes pneumococcus colonization in the nasopharynx as well as invasion into deeper tissues, thus significantly contributing to pathogenesis. It is known that the two-component system 07 induces the N-glycan metabolizing genes; however, how TCS07 is activated remains unknown. This study reveals that formate, the anaerobic fermentation metabolite of pneumococcus, is a novel activator of the response regulator (RR) 07. Although the high expression of N-glycan degradation genes promotes pneumococcal colonization in the nasopharynx and pathogenesis, this reduces pneumococcal growth fitness in glucose as indicated in this work. Notably, the presence of Pn-AqpC, an oxygen-transporting aquaglyceroporin, enables pneumococcus to maintain glucose homolactic acid fermentation, thus reducing formate production, maintaining RR07 inactivation, and controlling N-glycan degrading genes at a non-induced status. Thus, this study highlights a novel fermentation metabolism pattern linking TCS-regulated carbohydrate utilization strategies as a trade-off between the fitness and the pathogenicity of pneumococcus.
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Liang J, van Kranenburg R, Bolhuis A, Leak DJ. Removing carbon catabolite repression in Parageobacillus thermoglucosidasius DSM 2542. Front Microbiol 2022; 13:985465. [PMID: 36338101 PMCID: PMC9631020 DOI: 10.3389/fmicb.2022.985465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/21/2022] Open
Abstract
Parageobacillus thermoglucosidasius is a thermophilic bacterium of interest for lignocellulosic biomass fermentation. However, carbon catabolite repression (CCR) hinders co-utilization of pentoses and hexoses in the biomass substrate. Hence, to optimize the fermentation process, it is critical to remove CCR in the fermentation strains with minimal fitness cost. In this study, we investigated whether CCR could be removed from P. thermoglucosidasius DSM 2542 by mutating the Ser46 regulatory sites on HPr and Crh to a non-reactive alanine residue. It was found that neither the ptsH1 (HPr-S46A) nor the crh1 (Crh-S46A) mutation individually eliminated CCR in P. thermoglucosidasius DSM 2542. However, it was not possible to generate a ptsH1 crh1 double mutant. While the Crh-S46A mutation had no obvious fitness effect in DSM 2542, the ptsH1 mutation had a negative impact on cell growth and sugar utilization under fermentative conditions. Under these conditions, the ptsH1 mutation was associated with the production of a brown pigment, believed to arise from methylglyoxal production, which is harmful to cells. Subsequently, a less directed adaptive evolution approach was employed, in which DSM 2542 was grown in a mixture of 2-deoxy-D-glucose(2-DG) and xylose. This successfully removed CCR from P. thermoglucosidasius DSM 2542. Two selection strategies were applied to optimize the phenotypes of evolved strains. Genome sequencing identified key mutations affecting the PTS components PtsI and PtsG, the ribose operon repressor RbsR and adenine phosphoribosyltransferase APRT. Genetic complementation and bioinformatics analysis revealed that the presence of wild type rbsR and apt inhibited xylose uptake or utilization, while ptsI and ptsG might play a role in the regulation of CCR in P. thermoglucosidasius DSM 2542.
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Affiliation(s)
- Jinghui Liang
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
- *Correspondence: Jinghui Liang
| | - Richard van Kranenburg
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
- Corbion, Gorinchem, Netherlands
| | - Albert Bolhuis
- Department of Pharmacy and Pharmacology, Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom
| | - David J. Leak
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath, United Kingdom
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Deciphering the transcriptional regulation of the catabolism of lignin-derived aromatics in Rhodococcus opacus PD630. Commun Biol 2022; 5:1109. [PMID: 36261484 DOI: 10.1038/s42003-022-04069-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Rhodococcus opacus PD630 has considerable potential as a platform for valorizing lignin due to its innate "biological funneling" pathways. However, the transcriptional regulation of the aromatic catabolic pathways and the mechanisms controlling aromatic catabolic operons in response to different aromatic mixtures are still underexplored. Here, we identified and studied the transcription factors for aromatic degradation using GFP-based sensors and comprehensive deletion analyses. Our results demonstrate that the funneling pathways for phenol, guaiacol, 4-hydroxybenzoate, and vanillate are controlled by transcriptional activators. The two different branches of the β-ketoadipate pathway, however, are controlled by transcriptional repressors. Additionally, promoter activity assays revealed that the substrate hierarchy in R. opacus may be ascribed to the transcriptional cross-regulation of the individual aromatic funneling pathways. These results provide clues to clarify the molecule-level mechanisms underlying the complex regulation of aromatic catabolism, which facilitates the development of R. opacus as a promising chassis for valorizing lignin.
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Geng B, Jia X, Peng X, Han Y. Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering. Metab Eng Commun 2022; 15:e00211. [PMID: 36311477 PMCID: PMC9597109 DOI: 10.1016/j.mec.2022.e00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed. Hemicellulose is the main carbohydrate of biomass and has valuable applications. Hemicellulose is underutilized in conventional biomass refinery and pretreatment. Microbial and enzymatic catalysis were applied for hemicellulose utilization. Xylose is converted to value-added bioproducts by metabolic engineering.
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Affiliation(s)
- Biao Geng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China,Corresponding author. National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
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Liu Z, Wang Y, Liu S, Guo X, Zhao T, Wu J, Chen S. Boosting the Heterologous Expression of d-Allulose 3-Epimerase in Bacillus subtilis through Protein Engineering and Catabolite-Responsive Element Box Engineering. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12128-12134. [PMID: 36099523 DOI: 10.1021/acs.jafc.2c04800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As a natural sweetener with low calories and various physiological activities, d-allulose has drawn worldwide attention. Currently, d-allulose 3-epimerase (DAEase) is mainly used to catalyze the epimerization of d-fructose to d-allulose. Therefore, it is quite necessary to enhance the food-grade expression of DAEase to meet the surging market demand for d-allulose. In this study, initially, the promising variant H207L/D281G/C289R of Clostridium cellulolyticum H10 DAEase (CcDAEase) was generated by protein engineering, the specific activity and the T1/2 of which were 2.24-fold and 13.45-fold those of the CcDAEase wild type at 60 °C, respectively. After that, PamyE was determined as the optimal promoter for the recombinant expression of CcDAEase in Bacillus subtilis, and catabolite-responsive element (CRE) box engineering was further performed to eliminate the carbon catabolite repression (CCR) effect. Lastly, high-density fermentation was carried out and the final activity peaked at 4971.5 U mL-1, which is the highest expression level and could effectively promote the industrial production of DAEase. This research provides a theoretical basis and technical support for the molecular modification of DAEase and its efficient fermentation preparation.
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Affiliation(s)
- Zhanzhi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Yifan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Shuhan Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Xuehong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Tianlong Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, Jiangsu Province, China
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Fragoso-Jiménez JC, Gutierrez-Rios RM, Flores N, Martinez A, Lara AR, Delvigne F, Gosset G. Glucose consumption rate-dependent transcriptome profiling of Escherichia coli provides insight on performance as microbial factories. Microb Cell Fact 2022; 21:189. [PMID: 36100849 PMCID: PMC9472385 DOI: 10.1186/s12934-022-01909-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/27/2022] [Indexed: 11/21/2022] Open
Abstract
Background The modification of glucose import capacity is an engineering strategy that has been shown to improve the characteristics of Escherichia coli as a microbial factory. A reduction in glucose import capacity can have a positive effect on production strain performance, however, this is not always the case. In this study, E. coli W3110 and a group of four isogenic derivative strains, harboring single or multiple deletions of genes encoding phosphoenolpyruvate:sugar phosphotransferase system (PTS)-dependent transporters as well as non-PTS transporters were characterized by determining their transcriptomic response to reduced glucose import capacity. Results These strains were grown in bioreactors with M9 mineral salts medium containing 20 g/L of glucose, where they displayed specific growth rates ranging from 0.67 to 0.27 h−1, and specific glucose consumption rates (qs) ranging from 1.78 to 0.37 g/g h. RNA-seq analysis revealed a transcriptional response consistent with carbon source limitation among all the mutant strains, involving functions related to transport and metabolism of alternate carbon sources and characterized by a decrease in genes encoding glycolytic enzymes and an increase in gluconeogenic functions. A total of 107 and 185 genes displayed positive and negative correlations with qs, respectively. Functions displaying positive correlation included energy generation, amino acid biosynthesis, and sugar import. Conclusion Changes in gene expression of E. coli strains with impaired glucose import capacity could be correlated with qs values and this allowed an inference of the physiological state of each mutant. In strains with lower qs values, a gene expression pattern is consistent with energy limitation and entry into the stationary phase. This physiological state could explain why these strains display a lower capacity to produce recombinant protein, even when they show very low rates of acetate production. The comparison of the transcriptomes of the engineered strains employed as microbial factories is an effective approach for identifying favorable phenotypes with the potential to improve the synthesis of biotechnological products. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01909-y.
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Affiliation(s)
- Juan Carlos Fragoso-Jiménez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Rosa María Gutierrez-Rios
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Ciudad de Mexico, México
| | - Frank Delvigne
- Terra Research and Teaching Centre, Microbial Processes and Interactions (MiPI) Gembloux Agro‑Bio Tech, University of Liège, Gembloux, Belgium
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
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Johnston ML, Bonett EM, DeColli AA, Freel Meyers CL. Antibacterial Target DXP Synthase Catalyzes the Cleavage of d-Xylulose 5-Phosphate: a Study of Ketose Phosphate Binding and Ketol Transfer Reaction. Biochemistry 2022; 61:1810-1823. [PMID: 35998648 PMCID: PMC9531112 DOI: 10.1021/acs.biochem.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial enzyme 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) catalyzes the formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) in a thiamin diphosphate (ThDP)-dependent manner. In addition to its role in isoprenoid biosynthesis, DXP is required for ThDP and pyridoxal phosphate biosynthesis. Due to its function as a branch-point enzyme and its demonstrated substrate and catalytic promiscuity, we hypothesize that DXPS could be key for bacterial adaptation in the dynamic metabolic landscape during infection. Prior work in the Freel Meyers laboratory has illustrated that DXPS displays relaxed specificity toward donor and acceptor substrates and varies acceptor specificity according to the donor used. We have reported that DXPS forms dihydroxyethyl (DHE)ThDP from ketoacid or aldehyde donor substrates via decarboxylation and deprotonation, respectively. Here, we tested other DHE donors and found that DXPS cleaves d-xylulose 5-phosphate (X5P) at C2-C3, producing DHEThDP through a third mechanism involving d-GAP elimination. We interrogated DXPS-catalyzed reactions using X5P as a donor substrate and illustrated (1) production of a semi-stable enzyme-bound intermediate and (2) O2, H+, and d-erythrose 4-phosphate act as acceptor substrates, highlighting a new transketolase-like activity of DXPS. Furthermore, we examined X5P binding to DXPS and suggest that the d-GAP binding pocket plays a crucial role in X5P binding and turnover. Overall, this study reveals a ketose-cleavage reaction catalyzed by DXPS, highlighting the remarkable flexibility for donor substrate usage by DXPS compared to other C-C bond-forming enzymes.
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Affiliation(s)
- Melanie L. Johnston
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eucolona M. Bonett
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Caren L. Freel Meyers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Gonzalez-Nayeck AC, Mohr W, Tang T, Sattin S, Parenteau MN, Jahnke LL, Pearson A. Absence of canonical trophic levels in a microbial mat. GEOBIOLOGY 2022; 20:726-740. [PMID: 35831948 DOI: 10.1111/gbi.12511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/16/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
In modern ecosystems, the carbon stable isotope (δ13 C) ratios of consumers generally conform to the principle "you are what you eat, +1‰." However, this metric may not apply to microbial mat systems where diverse communities, using a variety of carbon substrates via multiple assimilation pathways, live in close physical association and phagocytosis is minimal or absent. To interpret the δ13 C record of the Proterozoic and early Paleozoic, when mat-based productivity likely was widespread, it is necessary to understand how a microbially driven producer-consumer structure affects the δ13 C compositions of biomass and preservable lipids. Protein Stable Isotope Fingerprinting (P-SIF) is a recently developed method that allows measurement of the δ13 C values of whole proteins, separated from environmental samples and identified taxonomically via proteomics. Here, we use P-SIF to determine the trophic relationships in a microbial mat sample from Chocolate Pots Hot Springs, Yellowstone National Park (YNP), USA. In this mat, proteins from heterotrophic bacteria are indistinguishable from cyanobacterial proteins, indicating that "you are what you eat, +1‰" is not applicable. To explain this finding, we hypothesize that sugar production and consumption dominate the net ecosystem metabolism, yielding a community in which producers and consumers share primary photosynthate as a common resource. This idea was validated by confirming that glucose moieties in exopolysaccharide were equal in δ13 C composition to both cyanobacterial and heterotrophic proteins, and by confirming that highly 13 C-depleted fatty acids (FAs) of Cyanobacteria dominate the lipid pool, consistent with flux-balance expectations for systems that overproduce primary photosynthate. Overall, the results confirm that the δ13 C composition of microbial biomass and lipids is tied to specific metabolites, rather than to autotrophy versus heterotrophy or to individual trophic levels. Therefore, we suggest that aerobic microbial heterotrophy is simply a case of "you are what you eat."
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Affiliation(s)
- Ana C Gonzalez-Nayeck
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Tiantian Tang
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
- State Key Laboratory of Marine Environmental Science (Xiamen University), Xiamen, Fujian, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Sarah Sattin
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
| | | | - Linda L Jahnke
- NASA Ames Research Center, Moffett Field, California, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts, USA
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134
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Kutnu M, İşlerel ET, Tunçbağ N, Özcengiz G. Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis. Integr Biol (Camb) 2022; 14:99-110. [PMID: 35901454 DOI: 10.1093/intbio/zyac010] [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: 04/19/2021] [Revised: 12/07/2021] [Accepted: 01/05/2022] [Indexed: 06/15/2023]
Abstract
The Gram-positive bacterium Bacillus subtilis produces a diverse range of secondary metabolites with different structures and activities. Among them, bacilysin is an enzymatically synthesized dipeptide that consists of L-alanine and L-anticapsin. Previous research by our group has suggested bacilysin's role as a pleiotropic molecule in its producer, B. subtilis PY79. However, the nature of protein interactions in the absence of bacilysin has not been defined. In the present work, we constructed a protein-protein interaction subnetwork by using Omics Integrator based on our recent comparative proteomics data obtained from a bacilysin-silenced strain, OGU1. Functional enrichment analyses on the resulting networks pointed to certain putatively perturbed pathways such as citrate cycle, quorum sensing and secondary metabolite biosynthesis. Various molecules, which were absent from the experimental data, were included in the final network. We believe that this study can guide further experiments in the identification and confirmation of protein-protein interactions in B. subtilis.
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Affiliation(s)
- Meltem Kutnu
- Department of Biological Sciences/Molecular Biology and Genetics, Middle East Technical University, Ankara 06800, Turkey
| | - Elif Tekin İşlerel
- Department of Biological Sciences/Molecular Biology and Genetics, Middle East Technical University, Ankara 06800, Turkey
- Department of Medical Microbiology, Faculty of Medicine, Maltepe University, Istanbul 34857, Turkey
| | - Nurcan Tunçbağ
- Department of Chemical and Biological Engineering, Koc University, Istanbul 34450, Turkey
| | - Gülay Özcengiz
- Department of Biological Sciences/Molecular Biology and Genetics, Middle East Technical University, Ankara 06800, Turkey
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135
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Fu H, Zhang H, Guo X, Yang L, Wang J. Elimination of carbon catabolite repression in Clostridium tyrobutyricum for enhanced butyric acid production from lignocellulosic hydrolysates. BIORESOURCE TECHNOLOGY 2022; 357:127320. [PMID: 35589044 DOI: 10.1016/j.biortech.2022.127320] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Clostridium tyrobutyricum, a gram-positive anaerobic bacterium, is recognized as the promising butyric acid producer. But, the existence of carbon catabolite repression (CCR) is the major drawback for C. tyrobutyricum to efficiently use the lignocellulosic biomass. In this study, the xylose pathway genes were first identified and verified. Then, the potential regulatory mechanisms of CCR in C. tyrobutyricum were proposed and the predicted engineering targets were experimental validated. Inactivation of hprK blocked the CcpA-mediated CCR and resulted in simultaneous conversion of glucose and xylose, although xylose consumption was severe lagging behind. Deletion of xylR further shortened the lag phase of xylose utilization. When hprK and xylR were inactivated together, the CCR in C. tyrobutyricum was completely eliminated. Consequently, ATCC 25755/ΔhprKΔxylR showed significant increase in butyrate productivity (1.8 times faster than the control) and excellent butyric acid fermentation performance using both mixed sugars (11.0-11.9 g/L) and undetoxified lignocellulosic hydrolysates (12.4-13.4 g/L).
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Affiliation(s)
- Hongxin Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China
| | - Huihui Zhang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaolong Guo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Lu Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China; State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510006, China.
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136
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Koga R, Moriyama M, Onodera-Tanifuji N, Ishii Y, Takai H, Mizutani M, Oguchi K, Okura R, Suzuki S, Gotoh Y, Hayashi T, Seki M, Suzuki Y, Nishide Y, Hosokawa T, Wakamoto Y, Furusawa C, Fukatsu T. Single mutation makes Escherichia coli an insect mutualist. Nat Microbiol 2022; 7:1141-1150. [PMID: 35927448 PMCID: PMC9352592 DOI: 10.1038/s41564-022-01179-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023]
Abstract
Microorganisms often live in symbiosis with their hosts, and some are considered mutualists, where all species involved benefit from the interaction. How free-living microorganisms have evolved to become mutualists is unclear. Here we report an experimental system in which non-symbiotic Escherichia coli evolves into an insect mutualist. The stinkbug Plautia stali is typically associated with its essential gut symbiont, Pantoea sp., which colonizes a specialized symbiotic organ. When sterilized newborn nymphs were infected with E. coli rather than Pantoea sp., only a few insects survived, in which E. coli exhibited specific localization to the symbiotic organ and vertical transmission to the offspring. Through transgenerational maintenance with P. stali, several hypermutating E. coli lines independently evolved to support the host's high adult emergence and improved body colour; these were called 'mutualistic' E. coli. These mutants exhibited slower bacterial growth, smaller size, loss of flagellar motility and lack of an extracellular matrix. Transcriptomic and genomic analyses of 'mutualistic' E. coli lines revealed independent mutations that disrupted the carbon catabolite repression global transcriptional regulator system. Each mutation reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that single carbon catabolite repression mutations can make E. coli an insect mutualist. These findings provide an experimental system for future work on host-microbe symbioses and may explain why microbial mutualisms are omnipresent in nature.
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Affiliation(s)
- Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Naoko Onodera-Tanifuji
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoshiko Ishii
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiroki Takai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masaki Mizutani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kohei Oguchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Reiko Okura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Suzuki
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yudai Nishide
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Takahiro Hosokawa
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Yuichi Wakamoto
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Chikara Furusawa
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan. .,Department of Biological Sciences, The University of Tokyo, Tokyo, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
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137
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Dhamale T, Saha BK, Papade SE, Singh S, Phale PS. A unique global metabolic trait of Pseudomonas bharatica CSV86 T: metabolism of aromatics over simple carbon sources and co-metabolism with organic acids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35925665 DOI: 10.1099/mic.0.001206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Hierarchical utilization of substrate by microbes (utilization of simple carbon sources prior to complex ones) poses a major limitation to the efficient remediation of aromatic pollutants. Aromatic compounds, being complex and reduced in nature, appear to be a deferred choice as the carbon source in the presence of a plethora of simple organic compounds in the environment. The soil bacterium Pseudomonas bharatica CSV86T displays a unique carbon source utilization hierarchy. It preferentially utilizes aromatics over glucose and co-metabolizes them with succinate or pyruvate (Basu et al., 2006, Applied and Environmental Microbiology, 72 : 22226-2230). In the present study, the substrate utilization hierarchy for strain CSV86T was tested for additional simple carbon sources such as glycerol, acetate, and tri-carboxylic acid (TCA) cycle intermediates like α-ketoglutarate and fumarate. When grown on a mixture of aromatics (benzoate or naphthalene) plus glycerol, the strain displayed a diauxic growth profile with significantly high activity of aromatic utilization enzymes (catechol 1,2- or 2,3-dioxygenase, respectively) in the first-log phase. This suggests utilization of aromatics in the first-log phase followed by glycerol in the second-log phase. On a mixture of an aromatic plus organic acid (acetate, α-ketoglutarate or fumarate), the strain displayed a monoauxic growth profile, indicating co-metabolism. Interestingly, the presence of glycerol, acetate, α-ketoglutarate or fumarate does not repress metabolism/utilization of the aromatic. Thus, the substrate utilization hierarchy of strain CSV86T is aromatics=organic acids>glucose/glycerol, which is unique as compared to other Pseudomonas species, where degradation of aromatics is repressed by glycerol, glucose, acetate or organic acids, including TCA cycle intermediates. This novel substrate utilization hierarchy appears to be a global metabolic phenomenon in strain CSV86T, thus implying it to be an ideal host for metabolic engineering as well as for its potential application in bioremediation.
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Affiliation(s)
- Tushar Dhamale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Braja Kishor Saha
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Sandesh E Papade
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
| | - Srushti Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India.,Present address: Presently affiliated to TCR Therapeutics, Inc., 100 Binney Street, Cambridge, MA 02142, USA
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai 400 076, India
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138
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Insertion Sequence (IS)-Excision Enhancer (IEE)-Mediated IS Excision from the lacZ Gene Restores the Lactose Utilization Defect of Shiga Toxin-Producing Escherichia coli O121:H19 Strains and Is Responsible for Their Delayed Lactose Utilization Phenotype. Appl Environ Microbiol 2022; 88:e0076022. [PMID: 35913153 PMCID: PMC9397093 DOI: 10.1128/aem.00760-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lactose utilization is one of the general biochemical characteristics of Escherichia coli, and the lac operon is responsible for this phenotype, which can be detected on lactose-containing media, such as MacConkey agar, after 24 h of incubation. However, some Shiga toxin-producing E. coli (STEC) O121:H19 strains exhibit an unusual phenotype called delayed lactose utilization (DLU), in which lactose utilization can be detected after 48 h of cultivation but not after only 24 h of cultivation. Insertion of an insertion sequence (IS), IS600, into the lacZ gene appears to be responsible for the DLU phenotype, and exposure to lactose has been reported to be necessary to observe this phenotype, but the mechanism underlying these phenomena remains to be elucidated. Here, we performed detailed analyses of the lactose utilization abilities of a set of O121:H19 strains and their mutants and found that IS-excision enhancer (IEE)-mediated excision of IS600 reactivates the lacZ gene and that the selective proliferation of IS-cured subclones in lactose-supplemented culture medium is responsible for the expression of the DLU phenotype. In addition, we analyzed the patterns of IS insertion into the lacZ and iee genes in the global O121:H19 population and revealed that while there are O121:H19 strains or lineage/sublineages that contain the IS insertion into iee or intact lacZ and thus do not show the DLU phenotype, most currently circulating O121:H19 strains contain IS600-inserted lacZ and intact iee and thus exhibit this phenotype. IMPORTANCE Insertion sequences (ISs) can modulate gene expression by gene inactivation or activation. While phenotypic changes due to IS insertion/transposition are frequently observed, gene reactivation by precise or simple IS excision rarely occurs. In this study, we show that IS600 is excised from the lacZ gene by IS-excision enhancer (IEE) during the cultivation of Shiga toxin-producing Escherichia coli (STEC) O121:H19 strains that show an unusual phenotype called delayed lactose utilization (DLU). This excision rescued their lactose utilization defect, and the subsequent selective proliferation of IS-cured subclones in lactose-containing medium resulted in the expression of the DLU phenotype. As we also show that most currently circulating O121:H19 strains exhibit this phenotype, this study not only provides information helpful for the isolation and identification of O121:H19 STEC but also offers novel insights into the roles of IS and IEE in the generation of phenotypic variation in bacterial populations.
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139
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Zagrodnik R, Duber A, Seifert K. Dark-fermentative hydrogen production from synthetic lignocellulose hydrolysate by a mixed bacterial culture: The relationship between hydraulic retention time and pH conditions. BIORESOURCE TECHNOLOGY 2022; 358:127309. [PMID: 35569715 DOI: 10.1016/j.biortech.2022.127309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
This study assessed the effect of hydraulic retention time (HRT) ranging from 24 to 3 h on continuous dark-fermentative H2 production in four bioreactors operated at pH 5.0, 5.5, 6.0 and 6.5. A mixture of cellobiose, xylose and arabinose was used as the substrate. The highest hydrogen production rate between HRTs of 24 and 12 h was observed at pH 6.5, while at HRT below 12 h at pH 6.0. At a HRT of 3 h it reached 11.4 L H2/L-d. Thus, the optimum pH for H2 production depends on the HRT. The highest sugar utilization was obtained at pH 6.0 and 6.5 and decreased in the following order: cellobiose > xylose > arabinose. The pH conditions, in contrast to HRT, were found to have a significant influence on the bacterial composition. Low diversity in bacterial culture dominated by the Clostridium genus allows for stable and high H2 production performance.
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Affiliation(s)
- Roman Zagrodnik
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland.
| | - Anna Duber
- Institute of Environmental Engineering and Building Installations, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965 Poznan, Poland
| | - Krystyna Seifert
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznan, Poland
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140
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Cai X, Li X, Qin J, Zhang Y, Yan B, Cai J. Gene rppA co-regulated by LRR, SigA, and CcpA mediates antibiotic resistance in Bacillus thuringiensis. Appl Microbiol Biotechnol 2022; 106:5687-5699. [PMID: 35906441 DOI: 10.1007/s00253-022-12090-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: 06/25/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022]
Abstract
Antibiotic resistance genes are usually tightly controlled by transcription factors and RNA regulatory elements including sRNAs, riboswitches, and attenuators, and their expression is activated to respond to antibiotic exposure. In previous work, we revealed that the rppA gene is regulated by attenuator LRR and two mistranslation products in Bacillus thuringiensis BMB171. However, its function and promoter regulation is still not precise. In this study, we demonstrated that the encoding product of the rppA gene acts as an ARE1 ABC-F protein and confers resistance to antibiotics virginiamycin M1 and lincomycin when overexpressed. Besides the reported attenuator LRR, the expression of the rppA gene is controlled by the sigma factor SigA and a global transcription factor CcpA. Consequently, its promoter activity is mainly maintained at the stationary phase of cell growth and inhibited in the presence of glucose. Our study revealed the function and regulation of the rppA gene in detail. KEY POINTS: • The RppA protein acts as an ARE1 ABC-F protein • The rppA gene confers resistance to antibiotics virginiamycin M1 and lincomycin when overexpressed • The expression of the rppA gene is regulated by the sigma factor SigA and the pleiotropic regulator CcpA.
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Affiliation(s)
- Xia Cai
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xuelian Li
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jiaxin Qin
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yizhuo Zhang
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Bing Yan
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jun Cai
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, 300071, China.
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, 300071, China.
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141
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Choi KR, Yu HE, Lee H, Lee SY. Improved production of heme using metabolically engineered Escherichia coli. Biotechnol Bioeng 2022; 119:3178-3193. [PMID: 35892195 DOI: 10.1002/bit.28194] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/29/2022] [Accepted: 07/24/2022] [Indexed: 11/05/2022]
Abstract
Heme has recently attracted much attention due to its promising applications in food and healthcare industries. However, the current titers and productivities of heme produced by recombinant microorganisms are not high enough for a wide range of applications. In this study, the process for the fermentation of the metabolically engineered E. coli HAEM7 strain was optimized for the high-level production of heme. To improve the production of heme, different carbon sources, iron concentration in the medium, pH control strategies, induction points, and iron content in feeding solution were examined. Moreover, strategies of increasing cell density, regular iron supplementation, and supply of excess feeding solution were developed to further improve the production of heme. In the optimized fermentation process, the HAEM7 strain produced 1.03 g/L heme with a productivity of 21.5 mg/L/h. The fermentation process and strategies reported here will expedite establishing industry-level production of heme. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Kyeong Rok Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea
| | - Hye Eun Yu
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hoseong Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.,BioProcess Engineering Research Center, KAIST, Daejeon, 34141, Republic of Korea.,BioInformatics Research Center, KAIST Institute for the BioCentury, KAIST Institute for Artificial Intelligence, KAIST, Daejeon, 34141, Republic of Korea
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142
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Interplay of CodY and CcpA in Regulating Central Metabolism and Biofilm Formation in Staphylococcus aureus. J Bacteriol 2022; 204:e0061721. [PMID: 35735992 PMCID: PMC9295537 DOI: 10.1128/jb.00617-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Staphylococcus aureus is a medically important pathogen with high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, namely, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development, we constructed and characterized the codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control the cellular metabolic status by altering carbon flux through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of extracellular DNA (eDNA) into the biofilm matrix, whereas disrupting codY resulted in a robust structured biofilm tethered together with eDNA and polysaccharide intercellular adhesin (PIA). Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and reduces eDNA release in the double mutant. Compared with the inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, the codY ccpA mutant produced large amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Combined, the results of this study suggest that the coordinated action of CodY and CcpA modulate central metabolism, virulence gene expression, and biofilm-associated genes to optimize growth on preferred carbon sources until starvation sets in. IMPORTANCE Staphylococcus aureus is a leading cause of biofilm-associated infections, including infective endocarditis, worldwide. A greater understanding of metabolic forces driving biofilm formation in S. aureus is essential for the identification of novel therapeutic targets and for the development of new strategies to combat this medically important pathogen. This study characterizes the interplay and regulation of central metabolism and biofilm development by two global transcriptional regulators, CodY and CcpA. We found that the lack of CcpA and/or CodY have different impacts on intracellular metabolic status leading to a formation of morphologically altered biofilms. Overall, the results of this study provide new insights into our understanding of metabolism-mediated regulation of biofilm development in S. aureus.
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143
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Signal binding at both modules of its dCache domain enables the McpA chemoreceptor of Bacillus velezensis to sense different ligands. Proc Natl Acad Sci U S A 2022; 119:e2201747119. [PMID: 35858353 PMCID: PMC9303924 DOI: 10.1073/pnas.2201747119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Bacteria have evolved multiple signal transduction systems that permit an adaptation to changing environmental conditions. Chemoreceptor-based signaling cascades are very abundant in bacteria and are among the most complex signaling systems. Currently, our knowledge on the molecular features that determine signal recognition at chemoreceptors is limited. Chemoreceptor McpA of Bacillus velezensis SQR9 has been shown to mediate chemotaxis to a broad range of different ligands. Here we show that its ligand binding domain binds directly 13 chemoattractants. We provide support that organic acids and amino acids bind to the membrane-distal and membrane-proximal module of the dCache domain, respectively, whereas binding of sugars/sugar alcohols occurred at both modules. Structural biology studies combined with site-directed mutagenesis experiments have permitted to identify 10 amino acid residues that play key roles in the recognition of multiple ligands. Residues in membrane-distal and membrane-proximal regions were central for sensing organic acids and amimo acids, respectively, whereas all residues participated in sugars/sugar alcohol sensing. Most characterized chemoreceptors possess a narrow and well-defined ligand spectrum. We propose here a sensing mechanism involving both dCache modules that allows the integration of very diverse signals by a single chemoreceptor.
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144
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Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis. J Comput Aided Mol Des 2022; 36:507-520. [PMID: 35809194 PMCID: PMC9399212 DOI: 10.1007/s10822-022-00461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 06/14/2022] [Indexed: 12/02/2022]
Abstract
Enterococcus faecalis, a gram-positive bacterium, is among the most common nosocomial pathogens due to its limited susceptibility to antibiotics and its reservoir of the genes coding for virulence factors. Bacterial enzymes such as kinases and phosphorylases play important roles in diverse functions of a bacterial cell and, thus, are potential antibacterial drug targets. In Gram-positive bacteria, HPr Kinase/Phosphorylase (HPrK/P), a bifunctional enzyme is involved in the regulation of carbon catabolite repression by phosphorylating/dephosphorylating the histidine-containing phosphocarrier protein (HPr) at Ser46 residue. Deficiencies in HPrK/P function leads to severe defects in bacterial growth. This study aimed at identifying novel inhibitors of E. faecalis HPrK/P from a commercial compound library using structure-based virtual screening. The hit molecules were purchased and their effect on enzyme activity and growth of resistant E. faecalis was evaluated in vitro. Furthermore, docking and molecular dynamics simulations were performed to study the interactions of the hit compounds with HPrK/P. Among the identified hit molecules, two compounds inhibited the phosphorylation of HPr as well as significantly reduced the growth of resistant E. faecalis in vitro. These identified potential HPrK/P inhibitors open new research avenues towards the development of novel antimicrobials against resistant Gram-positive bacteria.
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145
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NupR Responding to Multiple Signals Is a Nucleoside Permease Regulator in Bacillus thuringiensis BMB171. Microbiol Spectr 2022; 10:e0154322. [PMID: 35862946 PMCID: PMC9430930 DOI: 10.1128/spectrum.01543-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleoside transport is essential for maintaining intracellular nucleoside and nucleobase homeostasis for living cells. Here, we identified an uncharacterized GntR/HutC family transcriptional regulator, NagR2, renamed NupR (nucleoside permease regulator), that mainly controls nucleoside transport in the Bacillus thuringiensis BMB171 strain. The deletion or overexpression of nupR affected the bacteria's utilization of guanosine, adenosine, uridine, and cytidine rather than thymidine. We further demonstrated that zinc ion is an effector for the NupR, dissociating NupR from its target DNA. Moreover, the expression of nupR is inhibited by NupR, ComK, and PurR, while it is promoted by CcpA. Also, a purine riboswitch located in its 5′ noncoding region influences the expression of nupR. Guanine is the ligand of the riboswitch, reducing the expression of nupR by terminating the transcription of nupR in advance. Hence, our results reveal an exquisite regulation mechanism enabling NupR to respond to multiple signals, control genes involved in nucleoside transport, and contribute to nucleoside substance utilization. Overall, this study provides essential clues for future studies exploring the function of the NupR homolog in other bacteria, such as Bacillus cereus, Bacillus anthracis, Klebsiella pneumoniae, and Streptococcus pneumoniae. IMPORTANCE The transport of nucleosides and their homeostasis within the cell are essential for growth and proliferation. Here, we have identified a novel transcription factor, NupR, which, to our knowledge, is the first GntR family transcription factor primarily involved in the regulation of nucleoside transport. Moreover, responding to diverse intracellular signals, NupR regulates nucleoside transport. It is vital for utilizing extracellular nucleosides and maintaining intracellular nucleoside homeostasis. NupR may also be involved in other pathways such as pH homeostasis, molybdenum cofactor biosynthesis, nitrate metabolism, and transport. In addition, nucleosides have various applications, such as antiviral drugs. Thus, the elucidation of the transport mechanism of nucleosides could be helpful for the construction of engineered strains for nucleoside production.
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146
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Mwiti G, Yeo IS, Jeong KH, Choi HS, Kim J. Activation of galactose utilization by the addition of glucose for the fermentation of agar hydrolysate using Lactobacillus brevis ATCC 14869. Biotechnol Lett 2022; 44:823-830. [PMID: 35727401 DOI: 10.1007/s10529-022-03267-6] [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: 12/21/2021] [Accepted: 05/31/2022] [Indexed: 11/02/2022]
Abstract
OBJECTIVE To investigate the application of carbon catabolite repression (CCR) relaxed Lactobacillus brevis ATCC 14869 in the utilization of agar hydrolysate to produce bioethanol and lactic acid through fermentation. RESULTS As a single carbon source, galactose was not metabolized by L. brevis. However, L. brevis consumed galactose simultaneous to glucose and ceased cell growth after depletion of glucose. For complete use of galactose from agar hydrolysis, glucose need to be periodically replenished into the growth medium. Overall, L. brevis successfully used agar hydrolysate and produced 17.2 g/L of ethanol and 31.9 g/L of lactic acid. The maximum specific cell growth rate on galactose and glucose mixture was the same with the glucose-only medium at 0.12 h-1. The molar product yields from glucose for lactic acid and ethanol were 1.02 and 0.95 respectively, equal to values obtained from the simultaneous utilization of glucose and galactose. CONCLUSION In contribution to the ongoing efforts to utilize marine biomass, the relaxed CCR in Lactobacillus brevis ATCC 14869 was herein exploited to produce bioethanol and lactic acid from red seaweed hydrolysates.
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Affiliation(s)
- Godfrey Mwiti
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-Ro, Yuseong-Gu, Daejeon, 34134, Republic of Korea
| | - In-Seok Yeo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Kyung-Hun Jeong
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-Ro, Yuseong-Gu, Daejeon, 34134, Republic of Korea
| | - Hyung-Seok Choi
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-Ro, Yuseong-Gu, Daejeon, 34134, Republic of Korea
| | - Jaehan Kim
- Department of Food and Nutrition, Chungnam National University, 99 Daehak-Ro, Yuseong-Gu, Daejeon, 34134, Republic of Korea.
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147
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Wang J, Li Z, Wang W, Pang S, Yao Y, Yuan F, Wang H, Xu Z, Pan G, Liu Z, Chen Y, Fan K. Dynamic Control Strategy to Produce Riboflavin with Lignocellulose Hydrolysate in the Thermophile Geobacillus thermoglucosidasius. ACS Synth Biol 2022; 11:2163-2174. [PMID: 35677969 DOI: 10.1021/acssynbio.2c00087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient utilization of both glucose and xylose, the two most abundant sugars in biomass hydrolysates, is one of the main objectives of biofermentation with lignocellulosic materials. The utilization of xylose is commonly inhibited by glucose, which is known as glucose catabolite repression (GCR). Here, we report a GCR-based dynamic control (GCR-DC) strategy aiming at better co-utilization of glucose and xylose, by decoupling the cell growth and biosynthesis of riboflavin as a product. Using the thermophilic strain Geobacillus thermoglucosidasius DSM 2542 as a host, we constructed additional riboflavin biosynthetic pathways that were activated by xylose but not glucose. The engineered strains showed a two-stage fermentation process. In the first stage, glucose was preferentially used for cell growth and no production of riboflavin was observed, while in the second stage where glucose was nearly depleted, xylose was effectively utilized for riboflavin biosynthesis. Using corn cob hydrolysate as a carbon source, the optimized riboflavin yields of strains DSM2542-DCall-MSS (full pathway dynamic control strategy) and DSM2542-DCrib (single-module dynamic control strategy) were 5.3- and 2.3-fold higher than that of the control strain DSM 2542 Rib-Gtg constitutively producing riboflavin, respectively. This GCR-DC strategy should also be applicable to the construction of cell factories that can efficiently use natural carbon sources with multiple sugar components for the production of high-value chemicals in future.
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Affiliation(s)
- Junyang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Pang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fang Yuan
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Huizhuan Wang
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Zhen Xu
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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148
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Cyle KT, Klein AR, Aristilde L, Martínez CE. Dynamic utilization of low-molecular-weight organic substrates across a microbial growth rate gradient. J Appl Microbiol 2022; 133:1479-1495. [PMID: 35665577 DOI: 10.1111/jam.15652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 11/28/2022]
Abstract
AIM Low-molecular-weight organic substances (LMWOSs) are at the nexus between microorganisms, plant roots, detritus, and the soil mineral matrix. Nominal oxidation state of carbon (NOSC) has been suggested a potential parameter for modeling microbial uptake rates of LMWOSs and the efficiency of carbon incorporation into new biomass. METHODS AND RESULTS In this study, we assessed the role of compound class and oxidation state on uptake kinetics and substrate-specific carbon use efficiency (SUE) during the growth of three model soil microorganisms, a fungal isolate (Penicillium spinulosum) and two bacterial isolates (Paraburkholderia solitsugae, and Ralstonia pickettii). Isolates were chosen that spanned a growth rate gradient (0.046-0.316 h-1 ) in media containing 34 common LMWOSs at realistically low initial concentrations (25 μM each). Clustered, co-utilization of LMWOSs occurred for all three organisms. Potential trends (p < 0.05) for early utilization of more oxidized substrates were present for the two bacterial isolates (P. solitsugae and R. pickettii), but high variability (R2 < 0.15) and a small effect of NOSC indicate these relationships are not useful for prediction. The SUEs of selected substrates ranged from 0.16-0.99 and there was no observed relationship between NOSC and SUE. CONCLUSION Our results do not provide compelling population-level support for NOSC as a predictive tool for either uptake kinetics or the efficiency of use of LMWOS in soil solution. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic strategies of organisms are likely more important than chemical identity in determining LMWOS cycling in soils. Previous community-level observations may be biased towards fast-responding bacterial community members.
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Affiliation(s)
- K Taylor Cyle
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Annaleise R Klein
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Australian Synchrotron, Australian Nuclear Science and Technology Organisation, Clayton, VIC 3168, Australia
| | - Ludmilla Aristilde
- Department of Biological and Environmental Engineering, Cornell University, Riley-Robb Hall, Ithaca, NY 14853.,Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, 60208, USA
| | - Carmen Enid Martínez
- Soil and Crop Sciences, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
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149
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Sequential uptake of aldoses over fructose and enhanced phosphate solubilization in Rhizobium sp. RM. Appl Microbiol Biotechnol 2022; 106:4251-4268. [DOI: 10.1007/s00253-022-11997-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/19/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
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150
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Mohapatra B, Nain S, Sharma R, Phale PS. Functional genome mining and taxono-genomics reveal eco-physiological traits and species distinctiveness of aromatic-degrading Pseudomonas bharatica sp. nov. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:464-474. [PMID: 35388632 DOI: 10.1111/1758-2229.13066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Assistive eco-physiological traits are necessary for microbes to adapt and colonize at polluted niches, enabling efficient clean-up. To demarcate species distinctiveness and eco-physiological traits of aromatic compounds metabolizing Pseudomonas sp. CSV86T (earlier identified as Pseudomonas putida), an Indian isolate from a petrol station soil, comparative genome mining, taxono-genomic, and physiological analyses were performed. A 6.79 Mbp genome (62.72 G + C mol%) of CSV86T encodes 6798 CDS and 238 unique genes. Naphthalene metabolism and Co-Zn-Cd resistance gene clusters were part of distinct genomic islands. Abundance of transporters (aromatics, organic acids, amino acids, and metals) and mobile elements (integrases, transposases, conjugative proteins) differentiated CSV86T from its closest relatives. Enhanced siderophore production for Fe-uptake during aromatic metabolism, indole acetic acid production, and fusaric acid resistance wasvalidated by genomic attributes. Full-length 16S-rRNA phylogeny revealed Pseudomonas japonica WLT as a closest relative of CSV86T . However, lower genomic indices (<97% gyrB-rpoB-rpoD homology, <90% ANI, <50% DNA-DNA relatedness) and taxonomic differences (assimilation of organic acids, amino acids, fatty acids composition) substantially differentiated CSV86T from its closest relatives, indicating it to be a novel species as Pseudomonas bharatica. Preferential metabolism of aromatics with advantageous eco-physiological traits renders CSV86T an ideal candidate for bioremediation and host for metabolic engineering.
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Affiliation(s)
- Balaram Mohapatra
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, Maharashtra, India
| | - Sonam Nain
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Rakesh Sharma
- Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR), Delhi, India
| | - Prashant S Phale
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Bombay, Powai, Mumbai, Maharashtra, India
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