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Grunfeld N, Levine E, Libby E. Experimental measurement and computational prediction of bacterial Hanks-type Ser/Thr signaling system regulatory targets. Mol Microbiol 2024; 122:152-164. [PMID: 38167835 PMCID: PMC11219531 DOI: 10.1111/mmi.15220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/05/2024]
Abstract
Bacteria possess diverse classes of signaling systems that they use to sense and respond to their environments and execute properly timed developmental transitions. One widespread and evolutionarily ancient class of signaling systems are the Hanks-type Ser/Thr kinases, also sometimes termed "eukaryotic-like" due to their homology with eukaryotic kinases. In diverse bacterial species, these signaling systems function as critical regulators of general cellular processes such as metabolism, growth and division, developmental transitions such as sporulation, biofilm formation, and virulence, as well as antibiotic tolerance. This multifaceted regulation is due to the ability of a single Hanks-type Ser/Thr kinase to post-translationally modify the activity of multiple proteins, resulting in the coordinated regulation of diverse cellular pathways. However, in part due to their deep integration with cellular physiology, to date, we have a relatively limited understanding of the timing, regulatory hierarchy, the complete list of targets of a given kinase, as well as the potential regulatory overlap between the often multiple kinases present in a single organism. In this review, we discuss experimental methods and curated datasets aimed at elucidating the targets of these signaling pathways and approaches for using these datasets to develop computational models for quantitative predictions of target motifs. We emphasize novel approaches and opportunities for collecting data suitable for the creation of new predictive computational models applicable to diverse species.
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Affiliation(s)
- Noam Grunfeld
- Department of Bioengineering, Northeastern University, Boston MA USA
| | - Erel Levine
- Department of Bioengineering, Northeastern University, Boston MA USA
- Department of Chemical Engineering, Northeastern University, Boston MA USA
| | - Elizabeth Libby
- Department of Bioengineering, Northeastern University, Boston MA USA
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2
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Cui L, Yang R, Huo D, Li L, Qu X, Wang J, Wang X, Liu H, Chen H, Wang X. Streptococcus pneumoniae extracellular vesicles aggravate alveolar epithelial barrier disruption via autophagic degradation of OCLN (occludin). Autophagy 2024; 20:1577-1596. [PMID: 38497494 PMCID: PMC11210924 DOI: 10.1080/15548627.2024.2330043] [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: 12/13/2023] [Accepted: 03/09/2024] [Indexed: 03/19/2024] Open
Abstract
Streptococcus pneumoniae (S. pneumoniae) represents a major human bacterial pathogen leading to high morbidity and mortality in children and the elderly. Recent research emphasizes the role of extracellular vesicles (EVs) in bacterial pathogenicity. However, the contribution of S. pneumoniae EVs (pEVs) to host-microbe interactions has remained unclear. Here, we observed that S. pneumoniae infections in mice led to severe lung injuries and alveolar epithelial barrier (AEB) dysfunction. Infections of S. pneumoniae reduced the protein expression of tight junction protein OCLN (occludin) and activated macroautophagy/autophagy in lung tissues of mice and A549 cells. Mechanically, S. pneumoniae induced autophagosomal degradation of OCLN leading to AEB impairment in the A549 monolayer. S. pneumoniae released the pEVs that could be internalized by alveolar epithelial cells. Through proteomics, we profiled the cargo proteins inside pEVs and found that these pEVs contained many virulence factors, among which we identified a eukaryotic-like serine-threonine kinase protein StkP. The internalized StkP could induce the phosphorylation of BECN1 (beclin 1) at Ser93 and Ser96 sites, initiating autophagy and resulting in autophagy-dependent OCLN degradation and AEB dysfunction. Finally, the deletion of stkP in S. pneumoniae completely protected infected mice from death, significantly alleviated OCLN degradation in vivo, and largely abolished the AEB disruption caused by pEVs in vitro. Overall, our results suggested that pEVs played a crucial role in the spread of S. pneumoniae virulence factors. The cargo protein StkP in pEVs could communicate with host target proteins and even hijack the BECN1 autophagy initiation pathway, contributing to AEB disruption and bacterial pathogenicity.Abbreviations: AEB: alveolarepithelial barrier; AECs: alveolar epithelial cells; ATG16L1: autophagy related 16 like 1; ATP:adenosine 5'-triphosphate; BafA1: bafilomycin A1; BBB: blood-brain barrier; CFU: colony-forming unit; co-IP: co-immunoprecipitation; CQ:chloroquine; CTRL: control; DiO: 3,3'-dioctadecylox-acarbocyanineperchlorate; DOX: doxycycline; DTT: dithiothreitol; ECIS: electricalcell-substrate impedance sensing; eGFP: enhanced green fluorescentprotein; ermR: erythromycin-resistance expression cassette; Ery: erythromycin; eSTKs: eukaryotic-like serine-threoninekinases; EVs: extracellular vesicles; HA: hemagglutinin; H&E: hematoxylin and eosin; HsLC3B: human LC3B; hpi: hours post-infection; IP: immunoprecipitation; KD: knockdown; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LC/MS: liquid chromatography-mass spectrometry; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MVs: membranevesicles; NC:negative control; NETs:neutrophil extracellular traps; OD: optical density; OMVs: outer membrane vesicles; PBS: phosphate-buffered saline; pEVs: S.pneumoniaeextracellular vesicles; protK: proteinase K; Rapa: rapamycin; RNAi: RNA interference; S.aureus: Staphylococcusaureus; SNF:supernatant fluid; sgRNA: single guide RNA; S.pneumoniae: Streptococcuspneumoniae; S.suis: Streptococcussuis; TEER: trans-epithelium electrical resistance; moi: multiplicity ofinfection; TEM:transmission electron microscope; TJproteins: tight junction proteins; TJP1/ZO-1: tight junction protein1; TSA: tryptic soy agar; WB: western blot; WT: wild-type.
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Affiliation(s)
- Luqing Cui
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Ruicheng Yang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, China
| | - Dong Huo
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Liang Li
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xinyi Qu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jundan Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xinyi Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Hulin Liu
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, China
| | - Xiangru Wang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, the Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Frontiers Science Center for Animal Breeding and Sustainable Production, Wuhan, China
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3
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Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [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: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
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Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
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4
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Frando A, Grundner C. More than two components: complexities in bacterial phosphosignaling. mSystems 2024; 9:e0028924. [PMID: 38591891 PMCID: PMC11097640 DOI: 10.1128/msystems.00289-24] [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] [Indexed: 04/10/2024] Open
Abstract
For over 40 years, the two-component systems (TCSs) have taken front and center in our thinking about the signaling mechanisms by which bacteria sense and respond to their environment. In contrast, phosphorylation on Ser/Thr and Tyr (O-phosphorylation) was long thought to be mostly restricted to eukaryotes and a somewhat accessory signaling mechanism in bacteria. Several recent studies exploring systems aspects of bacterial O-phosphorylation, however, now show that it is in fact pervasive, with some bacterial proteomes as highly phosphorylated as those of eukaryotes. Labile, non-canonical protein phosphorylation sites on Asp, Arg, and His are now also being identified in large numbers in bacteria and first cellular functions are discovered. Other phosphomodifications on Cys, Glu, and Lys remain largely unexplored. The surprising breadth and complexity of bacterial phosphosignaling reveals a vast signaling capacity, the full scope of which we may only now be beginning to understand but whose functions are likely to affect all aspects of bacterial physiology and pathogenesis.
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Affiliation(s)
- Andrew Frando
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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5
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Mishra AK, Thakare RP, Santani BG, Yabaji SM, Dixit SK, Srivastava KK. Unlocking the enigma of phenotypic drug tolerance: Mechanisms and emerging therapeutic strategies. Biochimie 2024; 220:67-83. [PMID: 38168626 DOI: 10.1016/j.biochi.2023.12.009] [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: 10/11/2023] [Revised: 12/09/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024]
Abstract
In the ongoing battle against antimicrobial resistance, phenotypic drug tolerance poses a formidable challenge. This adaptive ability of microorganisms to withstand drug pressure without genetic alterations further complicating global healthcare challenges. Microbial populations employ an array of persistence mechanisms, including dormancy, biofilm formation, adaptation to intracellular environments, and the adoption of L-forms, to develop drug tolerance. Moreover, molecular mechanisms like toxin-antitoxin modules, oxidative stress responses, energy metabolism, and (p)ppGpp signaling contribute to this phenomenon. Understanding these persistence mechanisms is crucial for predicting drug efficacy, developing strategies for chronic bacterial infections, and exploring innovative therapies for refractory infections. In this comprehensive review, we dissect the intricacies of drug tolerance and persister formation, explore their role in acquired drug resistance, and highlight emerging therapeutic approaches to combat phenotypic drug tolerance. Furthermore, we outline the future landscape of interventions for persistent bacterial infections.
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Affiliation(s)
- Alok K Mishra
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India; Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA, 01605, USA.
| | - Ritesh P Thakare
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India; Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA, 01605, USA
| | - Bela G Santani
- Department of Microbiology, Sant Gadge Baba Amravati University (SGBAU), Amravati, Maharashtra, India
| | - Shivraj M Yabaji
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA, USA
| | - Shivendra K Dixit
- Division of Medicine ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar Bareilly, Uttar Pradesh, 243122, India.
| | - Kishore K Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute (CDRI), Jankipuram Extension, Lucknow, Uttar Pradesh, 226031, India.
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6
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Frando A, Boradia V, Grundner C. Regulatory Intersection of Two-component System and Ser/Thr Protein Kinase Signaling in Mycobacterium tuberculosis. J Mol Biol 2024; 436:168379. [PMID: 38043732 PMCID: PMC11251531 DOI: 10.1016/j.jmb.2023.168379] [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: 08/28/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
Phosphosignaling in bacteria is mediated by two distinct systems, the two-component systems (TCSs) and the protein Ser/Thr/Tyr, or O-phosphorylation systems. These two arms of phosphosignaling are currently thought to be largely independent from one another. We mined a deep Mycobacterium tuberculosis (Mtb) phosphoproteome and identified over 170 O-phosphorylation sites on histidine kinases and response regulators of TCSs, suggesting that the two signaling pathways extensively intersect. Several TCSs were phosphorylated on multiple sites, and many by multiple Ser/Thr protein kinases, suggesting convergent and cooperative regulatory interactions. To test in which way these O-phosphorylation sites affect TCS activity, we reconstituted the NarSL phosphorelay in vitro. The Ser/Thr protein kinase PknL phosphorylated the histidine kinase NarS and activated its autophosphorylating activity. A phosphoablative mutation at the PknL phosphorylation site Thr380 resulted in low autophosphorylating activity, whereas a phosphomimetic mutation strongly activated autophosphorylation. The phosphomimetic mutation also resulted in more efficient phosphotransfer from NarS to the response regulator NarL and suppression of gene expression. These data show control of NarSL signaling by STPKs through a phosphoswitch and point to extensive, functional crosstalk between TCSs and O-phosphorylation.
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Affiliation(s)
- Andrew Frando
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Vishant Boradia
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Christoph Grundner
- Seattle Children's Research Institute, Seattle, WA, United States; Department of Pediatrics, University of Washington, Seattle, WA, United States; Department of Global Health, United States.
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7
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Hernandez Garcia A, Nair SK. Structure and Function of a Class III Metal-Independent Lanthipeptide Synthetase. ACS CENTRAL SCIENCE 2023; 9:1944-1956. [PMID: 37901177 PMCID: PMC10604976 DOI: 10.1021/acscentsci.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 10/31/2023]
Abstract
In bacteria, Ser/Thr protein kinase-like sequences are found as part of large multidomain polypeptides that biosynthesize lanthipeptides, a class of natural products distinguished by the presence of thioether cross-links. The kinase domain phosphorylates Ser or Thr residues in the peptide substrates. Subsequent β-elimination by a lyase domain yields electrophilic dehydroamino acids, which can undergo cyclase domain-catalyzed cyclization to yield conformationally restricted, bioactive compounds. Here, we reconstitute the biosynthetic pathway for a class III lanthipeptide from Bacillus thuringiensis NRRL B-23139, including characterization of a two-component protease for leader peptide excision. We also describe the first crystal structures of a class III lanthipeptide synthetase, consisting of the lyase, kinase, and cyclase domains, in various states including complexes with its leader peptide and nucleotide. The structure shows interactions between all three domains that result in an active conformation of the kinase domain. Biochemical analysis demonstrates that the three domains undergo movement upon binding of the leader peptide to establish interdomain allosteric interactions that stabilize this active form. These studies inform on the regulatory mechanism of substrate recognition and provide a framework for engineering of variants of biotechnological interest.
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Affiliation(s)
- Andrea Hernandez Garcia
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
| | - Satish K. Nair
- Department
of Biochemistry, University of Illinois
at Urbana−Champaign, Roger Adams
Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Roger Adams Laboratory, 600 S. Mathews Ave., Urbana, Illinois 61801, United States
- Carl
R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 W. Gregory Drive, Urbana, Illinois 61801, United States
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8
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Leasure CS, Grunenwald CM, Choby JE, Sauer JD, Skaar EP. Maintenance of heme homeostasis in Staphylococcus aureus through post-translational regulation of glutamyl-tRNA reductase. J Bacteriol 2023; 205:e0017123. [PMID: 37655914 PMCID: PMC10521356 DOI: 10.1128/jb.00171-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023] Open
Abstract
Staphylococcus aureus is an important human pathogen responsible for a variety of infections including skin and soft tissue infections, endocarditis, and sepsis. The combination of increasing antibiotic resistance in this pathogen and the lack of an efficacious vaccine underscores the importance of understanding how S. aureus maintains metabolic homeostasis in a variety of environments, particularly during infection. Within the host, S. aureus must regulate cellular levels of the cofactor heme to support enzymatic activities without encountering heme toxicity. Glutamyl tRNA reductase (GtrR), the enzyme catalyzing the first committed step in heme synthesis, is an important regulatory node of heme synthesis in Bacteria, Archaea, and Plantae. In many organisms, heme status negatively regulates the abundance of GtrR, controlling flux through the heme synthesis pathway. We identified two residues within GtrR, H32 and R214, that are important for GtrR-heme binding. However, in strains expressing either GtrRH32A or GtrRR214A, heme homeostasis was not perturbed, suggesting an alternative mechanism of heme synthesis regulation occurs in S. aureus. In this regard, we report that heme synthesis is regulated through phosphorylation and dephosphorylation of GtrR by the serine/threonine kinase Stk1 and the phosphatase Stp1, respectively. Taken together, these results suggest that the mechanisms governing staphylococcal heme synthesis integrate both the availability of heme and the growth status of the cell. IMPORTANCE Staphylococcus aureus represents a significant threat to human health. Heme is an iron-containing enzymatic cofactor that can be toxic at elevated levels. During infection, S. aureus must control heme levels to replicate and survive within the hostile host environment. We identified residues within a heme biosynthetic enzyme that are critical for heme binding in vitro; however, abrogation of heme binding is not sufficient to perturb heme homeostasis within S. aureus. This marks a divergence from previously reported mechanisms of heme-dependent regulation of the highly conserved enzyme glutamyl tRNA reductase (GtrR). Additionally, we link cell growth arrest to the modulation of heme levels through the post-translational regulation of GtrR by the kinase Stk1 and the phosphatase Stp1.
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Affiliation(s)
- Catherine S. Leasure
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Caroline M. Grunenwald
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jacob E. Choby
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John-Demian Sauer
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Gangwal A, Kumar N, Sangwan N, Dhasmana N, Dhawan U, Sajid A, Arora G, Singh Y. Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages. FEMS Microbiol Rev 2023; 47:fuad044. [PMID: 37533212 PMCID: PMC10465088 DOI: 10.1093/femsre/fuad044] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/04/2023] Open
Abstract
Protein phosphorylation is a universal mechanism regulating a wide range of cellular responses across all domains of life. The antagonistic activities of kinases and phosphatases can orchestrate the life cycle of an organism. The availability of bacterial genome sequences, particularly Bacillus species, followed by proteomics and functional studies have aided in the identification of putative protein kinases and protein phosphatases, and their downstream substrates. Several studies have established the role of phosphorylation in different physiological states of Bacillus species as they pass through various life stages such as sporulation, germination, and biofilm formation. The most common phosphorylation sites in Bacillus proteins are histidine, aspartate, tyrosine, serine, threonine, and arginine residues. Protein phosphorylation can alter protein activity, structural conformation, and protein-protein interactions, ultimately affecting the downstream pathways. In this review, we summarize the knowledge available in the field of Bacillus signaling, with a focus on the role of protein phosphorylation in its physiological processes.
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Affiliation(s)
- Aakriti Gangwal
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
| | - Nitika Sangwan
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Neha Dhasmana
- School of Medicine, New York University, 550 First Avenue New York-10016, New York, United States
| | - Uma Dhawan
- Department of Biomedical Science, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi-110075, India
| | - Andaleeb Sajid
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Gunjan Arora
- 300 Cedar St, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, New Haven CT, United States
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Faculty of Science, Delhi- 110007, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi-110007, India
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10
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Chen Y, Quirk NF, Tan S. Shining a light on bacterial environmental cue integration and its relation to metabolism. Mol Microbiol 2023; 120:71-74. [PMID: 37433048 PMCID: PMC10348474 DOI: 10.1111/mmi.15065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 07/13/2023]
Abstract
The ability of a bacterium to successfully colonize its host is dependent on proper adaptation to its local environment. Environmental cues are diverse in nature, ranging from ions to bacterial-produced signals, and to host immune responses that can also be exploited by the bacteria as cues. Simultaneously, bacterial metabolism must be matched to the carbon and nitrogen sources available at a given time and location. While initial characterization of a bacterium's response to a given environmental cue or its ability to utilize a particular carbon/nitrogen source requires study of the signal in question in isolation, actual infection poses a situation where multiple signals are present concurrently. This perspective focuses on the untapped potential in uncovering and understanding how bacteria integrate their response to multiple concurrent environmental cues, and in elucidating the possible intrinsic coordination of bacterial environmental response with its metabolism.
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Affiliation(s)
- Yue Chen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
| | - Natalia F. Quirk
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, USA
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Frando A, Boradia V, Gritsenko M, Beltejar C, Day L, Sherman DR, Ma S, Jacobs JM, Grundner C. The Mycobacterium tuberculosis protein O-phosphorylation landscape. Nat Microbiol 2023; 8:548-561. [PMID: 36690861 PMCID: PMC11376436 DOI: 10.1038/s41564-022-01313-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/16/2022] [Indexed: 01/25/2023]
Abstract
Bacterial phosphosignalling has been synonymous with two-component systems and their histidine kinases, but many bacteria, including Mycobacterium tuberculosis (Mtb), also code for Ser/Thr protein kinases (STPKs). STPKs are the main phosphosignalling enzymes in eukaryotes but the full extent of phosphorylation on protein Ser/Thr and Tyr (O-phosphorylation) in bacteria is untested. Here we explored the global signalling capacity of the STPKs in Mtb using a panel of STPK loss-of-function and overexpression strains combined with mass spectrometry-based phosphoproteomics. A deep phosphoproteome with >14,000 unique phosphosites shows that O-phosphorylation in Mtb is a vastly underexplored protein modification that affects >80% of the proteome and extensively interfaces with the transcriptional machinery. Mtb O-phosphorylation gives rise to an expansive, distributed and cooperative network of a complexity that has not previously been seen in bacteria and that is on par with eukaryotic phosphosignalling networks. A resource of >3,700 high-confidence direct substrate-STPK interactions and their transcriptional effects provides signalling context for >80% of Mtb proteins and allows the prediction and assembly of signalling pathways for mycobacterial physiology.
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Affiliation(s)
- Andrew Frando
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Vishant Boradia
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Claude Beltejar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Le Day
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - David R Sherman
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Shuyi Ma
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Jon M Jacobs
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Christoph Grundner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, USA.
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12
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Vincent MS, Ezraty B. Methionine oxidation in bacteria: A reversible post-translational modification. Mol Microbiol 2023; 119:143-150. [PMID: 36350090 DOI: 10.1111/mmi.15000] [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: 08/29/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Methionine is a sulfur-containing residue found in most proteins which are particularly susceptible to oxidation. Although methionine oxidation causes protein damage, it can in some cases activate protein function. Enzymatic systems reducing oxidized methionine have evolved in most bacterial species and methionine oxidation proves to be a reversible post-translational modification regulating protein activity. In this review, we inspect recent examples of methionine oxidation provoking protein loss and gain of function. We further speculate on the role of methionine oxidation as a multilayer endogenous antioxidant system and consider its potential consequences for bacterial virulence.
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Affiliation(s)
- Maxence S Vincent
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
| | - Benjamin Ezraty
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille University, CNRS, Marseille, France
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13
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A Novel Capsule Network with Attention Routing to Identify Prokaryote Phosphorylation Sites. Biomolecules 2022; 12:biom12121854. [PMID: 36551282 PMCID: PMC9775645 DOI: 10.3390/biom12121854] [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: 11/03/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
By denaturing proteins and promoting the formation of multiprotein complexes, protein phosphorylation has important effects on the activity of protein functional molecules and cell signaling. The regulation of protein phosphorylation allows microbes to respond rapidly and reversibly to specific environmental stimuli or niches, which is closely related to the molecular mechanisms of bacterial drug resistance. Accurate prediction of phosphorylation sites (p-site) of prokaryotes can contribute to addressing bacterial resistance and providing new perspectives for developing novel antibacterial drugs. Most existing studies focus on human phosphorylation sites, while tools targeting phosphorylation site identification of prokaryotic proteins are still relatively scarce. This study designs a capsule network-based prediction technique for p-site in prokaryotes. To address the poor scalability and unreliability of dynamic routing processes in the output space of capsule networks, a more reliable way is introduced to learn the consistency between capsules. We incorporate a self-attention mechanism into the routing algorithm to capture the global information of the capsule, reducing the computational effort while enriching the representation capability of the capsule. Aiming at the weak robustness of the model, EcapsP improves the prediction accuracy and stability by introducing shortcuts and unconditional reconfiguration. In addition, the study compares and analyzes the prediction performance based on word vectors, physicochemical properties, and mixing characteristics in predicting serine (Ser/S), threonine (Thr/T), and tyrosine (Tyr/Y) p-site. The comprehensive experimental results show that the accuracy of the developed technique is close to 70% for the identification of the three phosphorylation sites in prokaryotes. Importantly, in side-by-side comparisons with other state-of-the-art predictors, our method improves the Matthews correlation coefficient (MCC) by approximately 7%. The results demonstrate the superiority of EcapsP in terms of high performance and reliability.
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14
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Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9. BMC Ecol Evol 2022; 22:132. [PMID: 36357830 PMCID: PMC9650800 DOI: 10.1186/s12862-022-02088-5] [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] [Received: 04/14/2022] [Accepted: 10/29/2022] [Indexed: 11/12/2022] Open
Abstract
The arms race between humans and pathogens drives the evolution of the human genome. It is thus expected that genes from the interferon-regulatory factors family (IRFs), a critical family for anti-viral immune response, should be undergoing episodes of positive selection. Herein, we tested this hypothesis and found multiple lines of evidence for positive selection on the amino acid site Val129 (NP_006075.3:p.Ser129Val) of human IRF9. Interestingly, the ancestral reconstruction and population distribution analyses revealed that the ancestral state (Ser129) is conserved among mammals, while the derived positively selected state (Val129) was fixed before the “out-of-Africa” event ~ 500,000 years ago. The motif analysis revealed that this young amino acid (Val129) may serve as a dephosphorylation site of IRF9. Structural parallelism between homologous genes further suggested the functional effects underlying the dephosphorylation that may affect the immune activity of IRF9. This study provides a model in which a strong positive Darwinian selection drives a recent fixation of a hominin-specific amino acid leading to molecular adaptation involving dephosphorylation in an immune-responsive gene.
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15
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Garcia-Garcia T, Douché T, Giai Gianetto Q, Poncet S, El Omrani N, Smits WK, Cuenot E, Matondo M, Martin-Verstraete I. In-Depth Characterization of the Clostridioides difficile Phosphoproteome to Identify Ser/Thr Kinase Substrates. Mol Cell Proteomics 2022; 21:100428. [PMID: 36252736 PMCID: PMC9674922 DOI: 10.1016/j.mcpro.2022.100428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/13/2022] [Accepted: 10/13/2022] [Indexed: 11/17/2022] Open
Abstract
Clostridioides difficile is the leading cause of postantibiotic diarrhea in adults. During infection, the bacterium must rapidly adapt to the host environment by using survival strategies. Protein phosphorylation is a reversible post-translational modification employed ubiquitously for signal transduction and cellular regulation. Hanks-type serine/threonine kinases (STKs) and serine/threonine phosphatases have emerged as important players in bacterial cell signaling and pathogenicity. C. difficile encodes two STKs (PrkC and CD2148) and one phosphatase. We optimized a titanium dioxide phosphopeptide enrichment approach to determine the phosphoproteome of C. difficile. We identified and quantified 2500 proteins representing 63% of the theoretical proteome. To identify STK and serine/threonine phosphatase targets, we then performed comparative large-scale phosphoproteomics of the WT strain and isogenic ΔprkC, CD2148, Δstp, and prkC CD2148 mutants. We detected 635 proteins containing phosphorylated peptides. We showed that PrkC is phosphorylated on multiple sites in vivo and autophosphorylates in vitro. We were unable to detect a phosphorylation for CD2148 in vivo, whereas this kinase was phosphorylated in vitro only in the presence of PrkC. Forty-one phosphoproteins were identified as phosphorylated under the control of CD2148, whereas 114 proteins were phosphorylated under the control of PrkC including 27 phosphoproteins more phosphorylated in the ∆stp mutant. We also observed enrichment for phosphothreonine among the phosphopeptides more phosphorylated in the Δstp mutant. Both kinases targeted pathways required for metabolism, translation, and stress response, whereas cell division and peptidoglycan metabolism were more specifically controlled by PrkC-dependent phosphorylation in agreement with the phenotypes of the ΔprkC mutant. Using a combination of approaches, we confirmed that FtsK was phosphorylated in vivo under the control of PrkC and that Spo0A was a substrate of PrkC in vitro. This study provides a detailed mapping of kinase-substrate relationships in C. difficile, paving the way for the identification of new biomarkers and therapeutic targets.
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Affiliation(s)
- Transito Garcia-Garcia
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Thibaut Douché
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France
| | - Quentin Giai Gianetto
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France,Hub de bioinformatique et biostatistiques, Departement de Biologie computationelle, Institut Pasteur, Université Paris Cité, Paris, France
| | - Sandrine Poncet
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
| | - Nesrine El Omrani
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Elodie Cuenot
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France
| | - Mariette Matondo
- Plateforme Protéomique, Unité de Technologie et Service Spectrométrie de Masse pour la biologie, CNRS USR 2000, Institut Pasteur, Université Paris Cité, Paris, France,For correspondence: Isabelle Martin-Verstraete; Mariette Matondo
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogénese des Bactéries Anaérobies, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, Paris, France,Institut Universitaire de France, Paris, France,For correspondence: Isabelle Martin-Verstraete; Mariette Matondo
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16
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Role of serine/threonine protein phosphatase PrpN in the life cycle of Bacillus anthracis. PLoS Pathog 2022; 18:e1010729. [PMID: 35913993 PMCID: PMC9371265 DOI: 10.1371/journal.ppat.1010729] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 08/11/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
Reversible protein phosphorylation at serine/threonine residues is one of the most common protein modifications, widely observed in all kingdoms of life. The catalysts controlling this modification are specific serine/threonine kinases and phosphatases that modulate various cellular pathways ranging from growth to cellular death. Genome sequencing and various omics studies have led to the identification of numerous serine/threonine kinases and cognate phosphatases, yet the physiological relevance of many of these proteins remain enigmatic. In Bacillus anthracis, only one ser/thr phosphatase, PrpC, has been functionally characterized; it was reported to be non-essential for bacterial growth and survival. In the present study, we characterized another ser/thr phosphatase (PrpN) of B. anthracis by various structural and functional approaches. To examine its physiological relevance in B. anthracis, a null mutant strain of prpN was generated and shown to have defects in sporulation and reduced synthesis of toxins (PA and LF) and the toxin activator protein AtxA. We also identified CodY, a global transcriptional regulator, as a target of PrpN and ser/thr kinase PrkC. CodY phosphorylation strongly controlled its binding to the promoter region of atxA, as shown using phosphomimetic and phosphoablative mutants. In nutshell, the present study reports phosphorylation-mediated regulation of CodY activity in the context of anthrax toxin synthesis in B. anthracis by a previously uncharacterized ser/thr protein phosphatase–PrpN. Reversible protein phosphorylation at specific ser/thr residues causes conformational changes in the protein structure, thereby modulating its cellular activity. In B. anthracis, though the role of ser/thr phosphorylation is implicated in various cellular pathways including pathogenesis, till date only one STP (PrpC) has been functionally characterized. This manuscript reports functional characterization of another STP (PrpN) in B. anthracis and with the aid of a null mutant strain (BAS ΔprpN) we provide important insight regarding the role of PrpN in the life cycle of B. anthracis. We have also identified the global transcriptional regulator, CodY as a target of PrpN and PrkC, and for the first time showed the physiological relevance of CodY phosphorylation status in the regulation of anthrax toxin synthesis.
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17
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Giacalone D, Yap RE, Ecker AMV, Tan S. PrrA modulates Mycobacterium tuberculosis response to multiple environmental cues and is critically regulated by serine/threonine protein kinases. PLoS Genet 2022; 18:e1010331. [PMID: 35913986 PMCID: PMC9371303 DOI: 10.1371/journal.pgen.1010331] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/11/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to adapt to its surrounding environment is critical for the bacterium to successfully colonize its host. Transcriptional changes are a vital mechanism by which Mtb responds to key environmental signals experienced, such as pH, chloride (Cl-), nitric oxide (NO), and hypoxia. However, much remains unknown regarding how Mtb coordinates its response to the disparate signals seen during infection. Utilizing a transcription factor (TF) overexpression plasmid library in combination with a pH/Cl--responsive luciferase reporter, we identified the essential TF, PrrA, part of the PrrAB two-component system, as a TF involved in modulation of Mtb response to pH and Cl-. Further studies revealed that PrrA also affected Mtb response to NO and hypoxia, with prrA overexpression dampening induction of NO and hypoxia-responsive genes. PrrA is phosphorylated not just by its cognate sensor histidine kinase PrrB, but also by serine/threonine protein kinases (STPKs) at a second distinct site. Strikingly, a STPK-phosphoablative PrrA variant was significantly dampened in its response to NO versus wild type Mtb, disrupted in its ability to adaptively enter a non-replicative state upon extended NO exposure, and attenuated for in vivo colonization. Together, our results reveal PrrA as an important regulator of Mtb response to multiple environmental signals, and uncover a critical role of STPK regulation of PrrA in its function. Vital to successful host colonization by Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is the bacterium’s ability to respond and adapt to changes in its local environment during infection. Here, we discover that the essential transcription factor PrrA, part of the PrrAB two-component system (TCS), modulates Mtb response to four important environmental cues encountered within the host: pH, chloride, nitric oxide, and hypoxia. PrrA acts as a rheostat, adjusting the amplitude of Mtb gene expression changes upon bacterial exposure to each of the four environmental signals. Further, we reveal a critical impact of serine/threonine protein kinases (STPKs) on PrrA function, with prevention of STPK phosphorylation of PrrA disrupting adaptive response of Mtb to growth-inhibiting cues and attenuating the bacterium’s ability to colonize its host. Our work uncovers PrrA as a regulator with broad impact across environmental signals, and highlights how two regulatory systems, TCSs and STPKs, critically interact in coordinating Mtb response to environmental cues.
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Affiliation(s)
- David Giacalone
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | - Rochelle E. Yap
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Alwyn M. V. Ecker
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shumin Tan
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Graduate Program in Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- * E-mail:
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18
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Ulrych A, Fabrik I, Kupčík R, Vajrychová M, Doubravová L, Branny P. Cell Wall Stress Stimulates the Activity of the Protein Kinase StkP of Streptococcus pneumoniae, Leading to Multiple Phosphorylation. J Mol Biol 2021; 433:167319. [PMID: 34688688 DOI: 10.1016/j.jmb.2021.167319] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 12/28/2022]
Abstract
Streptococcus pneumoniae is an opportunistic human pathogen that encodes a single eukaryotic-type Ser/Thr protein kinase StkP and its functional counterpart, the protein phosphatase PhpP. These signaling enzymes play critical roles in coordinating cell division and growth in pneumococci. In this study, we determined the proteome and phosphoproteome profiles of relevant mutants. Comparison of those with the wild-type provided a representative dataset of novel phosphoacceptor sites and StkP-dependent substrates. StkP phosphorylates key proteins involved in cell division and cell wall biosynthesis in both the unencapsulated laboratory strain Rx1 and the encapsulated virulent strain D39. Furthermore, we show that StkP plays an important role in triggering an adaptive response induced by a cell wall-directed antibiotic. Phosphorylation of the sensor histidine kinase WalK and downregulation of proteins of the WalRK core regulon suggest crosstalk between StkP and the WalRK two-component system. Analysis of proteomic profiles led to the identification of gene clusters regulated by catabolite control mechanisms, indicating a tight coupling of carbon metabolism and cell wall homeostasis. The imbalance of steady-state protein phosphorylation in the mutants as well as after antibiotic treatment is accompanied by an accumulation of the global Spx regulator, indicating a Spx-mediated envelope stress response. In summary, StkP relays the perceived signal of cell wall status to key cell division and regulatory proteins, controlling the cell cycle and cell wall homeostasis.
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Affiliation(s)
- Aleš Ulrych
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Ivo Fabrik
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Rudolf Kupčík
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Marie Vajrychová
- Biomedical Research Center, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic.
| | - Linda Doubravová
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavel Branny
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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19
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King A, Blackledge MS. Evaluation of small molecule kinase inhibitors as novel antimicrobial and antibiofilm agents. Chem Biol Drug Des 2021; 98:1038-1064. [PMID: 34581492 PMCID: PMC8616828 DOI: 10.1111/cbdd.13962] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/24/2021] [Accepted: 09/15/2021] [Indexed: 12/25/2022]
Abstract
Antibiotic resistance is a global and pressing concern. Our current therapeutic arsenal is increasingly limited as bacteria are developing resistance at a rate that far outpaces our ability to create new treatments. Novel approaches to treating and curing bacterial infections are urgently needed. Bacterial kinases have been increasingly explored as novel drug targets and are poised for development into novel therapeutic agents to combat bacterial infections. This review describes several general classes of bacterial kinases that play important roles in bacterial growth, antibiotic resistance, and biofilm formation. General features of these kinase classes are discussed and areas of particular interest for the development of inhibitors will be highlighted. Small molecule kinase inhibitors are described and organized by phenotypic effect, spotlighting particularly interesting inhibitors with novel functions and potential therapeutic benefit. Finally, we provide our perspective on the future of bacterial kinase inhibition as a viable strategy to combat bacterial infections and overcome the pressures of increasing antibiotic resistance.
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Affiliation(s)
- Ashley King
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
| | - Meghan S. Blackledge
- Department of Chemistry, High Point University, One University Parkway, High Point, NC 27268
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20
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Nagarajan SN, Lenoir C, Grangeasse C. Recent advances in bacterial signaling by serine/threonine protein kinases. Trends Microbiol 2021; 30:553-566. [PMID: 34836791 DOI: 10.1016/j.tim.2021.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]
Abstract
It has been nearly three decades since the discovery of the first bacterial serine/threonine protein kinase (STPK). Since then, a blend of technological advances has led to the characterization of a multitude of STPKs and phosphorylation substrates in several bacterial species that finely regulate intricate signaling cascades. Years of intense research from several laboratories have demonstrated unexpected roles for serine/threonine phosphorylation, regulating not only bacterial growth and cell division but also antibiotic persistence, virulence and infection, metabolism, chromosomal biology, and cellular differentiation. This review aims to provide an account of the most recent and significant developments in this up and growing field in microbiology.
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Affiliation(s)
- Sathya Narayanan Nagarajan
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Cassandra Lenoir
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, IBCP building, 7 passage du Vercors, 69367 Lyon Cedex 07, France.
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21
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Liang C, Rios-Miguel AB, Jarick M, Neurgaonkar P, Girard M, François P, Schrenzel J, Ibrahim ES, Ohlsen K, Dandekar T. Staphylococcusaureus Transcriptome Data and Metabolic Modelling Investigate the Interplay of Ser/Thr Kinase PknB, Its Phosphatase Stp, the glmR/yvcK Regulon and the cdaA Operon for Metabolic Adaptation. Microorganisms 2021; 9:microorganisms9102148. [PMID: 34683468 PMCID: PMC8537086 DOI: 10.3390/microorganisms9102148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 01/17/2023] Open
Abstract
Serine/threonine kinase PknB and its corresponding phosphatase Stp are important regulators of many cell functions in the pathogen S. aureus. Genome-scale gene expression data of S. aureus strain NewHG (sigB+) elucidated their effect on physiological functions. Moreover, metabolic modelling from these data inferred metabolic adaptations. We compared wild-type to deletion strains lacking pknB, stp or both. Ser/Thr phosphorylation of target proteins by PknB switched amino acid catabolism off and gluconeogenesis on to provide the cell with sufficient components. We revealed a significant impact of PknB and Stp on peptidoglycan, nucleotide and aromatic amino acid synthesis, as well as catabolism involving aspartate transaminase. Moreover, pyrimidine synthesis was dramatically impaired by stp deletion but only slightly by functional loss of PknB. In double knockouts, higher activity concerned genes involved in peptidoglycan, purine and aromatic amino acid synthesis from glucose but lower activity of pyrimidine synthesis from glucose compared to the wild type. A second transcriptome dataset from S. aureus NCTC 8325 (sigB−) validated the predictions. For this metabolic adaptation, PknB was found to interact with CdaA and the yvcK/glmR regulon. The involved GlmR structure and the GlmS riboswitch were modelled. Furthermore, PknB phosphorylation lowered the expression of many virulence factors, and the study shed light on S. aureus infection processes.
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Affiliation(s)
- Chunguang Liang
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
| | - Ana B. Rios-Miguel
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
- Department of Environmental Microbiology, Institute of Water and Wetland Research, Radboud University, 6525 AJ Nijmegen, The Netherlands
| | - Marcel Jarick
- Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, University of Würzburg, 97080 Würzburg, Germany; (M.J.); (E.S.I.)
| | - Priya Neurgaonkar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
| | - Myriam Girard
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, CH-1211 Geneva 14, Switzerland; (M.G.); (P.F.); (J.S.)
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, CH-1211 Geneva 14, Switzerland; (M.G.); (P.F.); (J.S.)
| | - Jacques Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, University of Geneva Hospitals, CH-1211 Geneva 14, Switzerland; (M.G.); (P.F.); (J.S.)
| | - Eslam S. Ibrahim
- Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, University of Würzburg, 97080 Würzburg, Germany; (M.J.); (E.S.I.)
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Knut Ohlsen
- Institute for Molecular Infection Biology, Josef-Schneider-Straße 2/D15, University of Würzburg, 97080 Würzburg, Germany; (M.J.); (E.S.I.)
- Correspondence: (K.O.); (T.D.); Tel.: +49-931-31-82155 (K.O.); +49-931-31-84551 (T.D.)
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (C.L.); (A.B.R.-M.); (P.N.)
- Correspondence: (K.O.); (T.D.); Tel.: +49-931-31-82155 (K.O.); +49-931-31-84551 (T.D.)
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22
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Rajpurohit YS, Sharma DK, Misra HS. Involvement of Serine / Threonine protein kinases in DNA damage response and cell division in bacteria. Res Microbiol 2021; 173:103883. [PMID: 34624492 DOI: 10.1016/j.resmic.2021.103883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022]
Abstract
The roles of Serine/Threonine protein kinases (STPKs) in bacterial physiology, including bacterial responses to nutritional stresses and under pathogenesis have been well documented. STPKs roles in bacterial cell cycle regulation and DNA damage response have not been much emphasized, possibly because the LexA/RecA type SOS response became the synonym to DNA damage response and cell cycle regulation in bacteria. This review summarizes current knowledge of STPKs genetics, domain organization, and their roles in DNA damage response and cell division regulation in bacteria.
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Affiliation(s)
- Yogendra S Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India.
| | - Dhirendra Kumar Sharma
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Life Sciences, Homi Bhabha National Institute (DAE- Deemed University), Mumbai, 400094, India
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23
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Massier S, Robin B, Mégroz M, Wright A, Harper M, Hayes B, Cosette P, Broutin I, Boyce JD, Dé E, Hardouin J. Phosphorylation of Extracellular Proteins in Acinetobacter baumannii in Sessile Mode of Growth. Front Microbiol 2021; 12:738780. [PMID: 34659171 PMCID: PMC8517400 DOI: 10.3389/fmicb.2021.738780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/30/2021] [Indexed: 11/21/2022] Open
Abstract
Acinetobacter baumannii is a problematic nosocomial pathogen owing to its increasing resistance to antibiotics and its great ability to survive in the hospital environment, which is linked to its capacity to form biofilms. Structural and functional investigations of post-translational modifications, such as phosphorylations, may lead to identification of candidates for therapeutic targets against this pathogen. Here, we present the first S/T/Y phosphosecretome of two A. baumannii strains, the reference strain ATCC 17978 and the virulent multi-drug resistant strain AB0057, cultured in two modes of growth (planktonic and biofilm) using TiO2 chromatography followed by high resolution mass spectrometry. In ATCC 17978, we detected a total of 137 (97 phosphoproteins) and 52 (33 phosphoproteins) phosphosites in biofilm and planktonic modes of growth, respectively. Similarly, in AB0057, 155 (119 phosphoproteins) and 102 (74 phosphoproteins) phosphosites in biofilm and planktonic modes of growth were identified, respectively. Both strains in the biofilm mode of growth showed a higher number of phosphosites and phosphoproteins compared to planktonic growth. Several phosphorylated sites are localized in key regions of proteins involved in either drug resistance (β-lactamases), adhesion to host tissues (pilins), or protein secretion (Hcp). Site-directed mutagenesis of the Hcp protein, essential for type VI secretion system-mediated interbacterial competition, showed that four of the modified residues are essential for type VI secretion system activity.
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Affiliation(s)
- Sébastien Massier
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, Polymers, Biopolymers, Surfaces Laboratory, Rouen, France
- PISSARO Proteomic Facility, IRIB, Mont-Saint-Aignan, France
| | - Brandon Robin
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, Polymers, Biopolymers, Surfaces Laboratory, Rouen, France
| | - Marianne Mégroz
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Amy Wright
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Marina Harper
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Brooke Hayes
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Pascal Cosette
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, Polymers, Biopolymers, Surfaces Laboratory, Rouen, France
- PISSARO Proteomic Facility, IRIB, Mont-Saint-Aignan, France
| | | | - John D. Boyce
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
| | - Emmanuelle Dé
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, Polymers, Biopolymers, Surfaces Laboratory, Rouen, France
| | - Julie Hardouin
- Normandie Univ., UNIROUEN, INSA Rouen, CNRS, Polymers, Biopolymers, Surfaces Laboratory, Rouen, France
- PISSARO Proteomic Facility, IRIB, Mont-Saint-Aignan, France
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24
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Overview of protein phosphorylation in bacteria with a main focus on unusual protein kinases in Bacillus subtilis. Res Microbiol 2021; 172:103871. [PMID: 34500011 DOI: 10.1016/j.resmic.2021.103871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022]
Abstract
Protein phosphorylation is a post-translational modification that affects protein activity through the addition of a phosphate moiety by protein kinases or phosphotransferases. It occurs in all life forms. In addition to Hanks kinases found also in eukaryotes, bacteria encode membrane histidine kinases that, with their cognate response regulator, constitute two-component systems and phosphotransferases that phosphorylate proteins involved in sugar utilization on histidine and cysteine residues. In addition, they encode BY-kinases and arginine kinases that phosphorylate protein specifically on tyrosine and arginine residues respectively. They also possess unusual bacterial protein kinases illustrated here by examples from Bacillus subtilis.
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25
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Biochemical characterization of a recombinant acid phosphatase from Acinetobacter baumannii. PLoS One 2021; 16:e0252377. [PMID: 34077475 PMCID: PMC8172068 DOI: 10.1371/journal.pone.0252377] [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] [Received: 09/28/2020] [Accepted: 05/15/2021] [Indexed: 11/27/2022] Open
Abstract
Genomic sequence analysis of Acinetobacter baumannii revealed the presence of a putative Acid Phosphatase (AcpA; EC 3.1.3.2). A plasmid construct was made, and recombinant protein (rAcpA) was expressed in E. coli. PAGE analysis (carried out under denaturing/reducing conditions) of nickel-affinity purified protein revealed the presence of a near-homogeneous band of approximately 37 kDa. The identity of the 37 kDa species was verified as rAcpA by proteomic analysis with a molecular mass of 34.6 kDa from the deduced sequence. The dependence of substrate hydrolysis on pH was broad with an optimum observed at 6.0. Kinetic analysis revealed relatively high affinity for PNPP (Km = 90 μM) with Vmax, kcat, and Kcat/Km values of 19.2 pmoles s-1, 4.80 s-1(calculated on the basis of 37 kDa), and 5.30 x 104 M-1s-1, respectively. Sensitivity to a variety of reagents, i.e., detergents, reducing, and chelating agents as well as classic acid phosphatase inhibitors was examined in addition to assessment of hydrolysis of a number of phosphorylated compounds. Removal of phosphate from different phosphorylated compounds is supportive of broad, i.e., ‘nonspecific’ substrate specificity; although, the enzyme appears to prefer phosphotyrosine and/or peptides containing phosphotyrosine in comparison to serine and threonine. Examination of the primary sequence indicated the absence of signature sequences characteristic of Type A, B, and C nonspecific bacterial acid phosphatases.
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26
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The expanding world of protein kinase-like families in bacteria: forty families and counting. Biochem Soc Trans 2021; 48:1337-1352. [PMID: 32677675 DOI: 10.1042/bst20190712] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/24/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022]
Abstract
The protein kinase-like clan/superfamily is a large group of regulatory, signaling and biosynthetic enzymes that were historically regarded as typically eukaryotic proteins, although bacterial members have also been known for a long time. In this review, we explore the diversity of bacterial protein kinase like families, and discuss functional versatility of these enzymes, both the ones acting within the bacterial cell, and those acting within eukaryotic cells as effectors during infection. We focus on novel bacterial kinase-like families discovered in the last five years. A bioinformatics perspective is held here, hence sequence and structure comparison overview is presented, and also a comparison of genomic neighbourhoods of the families. We perform a phylum-level census of the families. Also, we discuss apparent pseudokinases that turned out to perform alternative catalytic functions by repurposing their atypical kinase-like active sites. We also highlight some 'unpopular' kinase-like families that await characterisation.
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27
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Luu LDW, Zhong L, Kaur S, Raftery MJ, Lan R. Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence. Front Cell Infect Microbiol 2021; 11:660280. [PMID: 33928046 PMCID: PMC8076611 DOI: 10.3389/fcimb.2021.660280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
The Bordetella genus is divided into two groups: classical and non-classical. Bordetella pertussis, Bordetella bronchiseptica and Bordetella parapertussis are known as classical bordetellae, a group of important human pathogens causing whooping cough or whooping cough-like disease and hypothesized to have evolved from environmental non-classical bordetellae. Bordetella infections have increased globally driving the need to better understand these pathogens for the development of new treatments and vaccines. One unexplored component in Bordetella is the role of serine, threonine and tyrosine phosphorylation. Therefore, this study characterized the phosphoproteome of classical bordetellae and examined its potential role in Bordetella biology and virulence. Applying strict identification of localization criteria, this study identified 70 unique phosphorylated proteins in the classical bordetellae group with a high degree of conservation. Phosphorylation was a key regulator of Bordetella metabolism with proteins involved in gluconeogenesis, TCA cycle, amino acid and nucleotide synthesis significantly enriched. Three key virulence pathways were also phosphorylated including type III secretion system, alcaligin synthesis and the BvgAS master transcriptional regulatory system for virulence genes in Bordetella. Seven new phosphosites were identified in BvgA with 6 located in the DNA binding domain. Of the 7, 4 were not present in non-classical bordetellae. This suggests that serine/threonine phosphorylation may play an important role in stabilizing/destabilizing BvgA binding to DNA for fine-tuning of virulence gene expression and that BvgA phosphorylation may be an important factor separating classical from non-classical bordetellae. This study provides the first insight into the phosphoproteome of classical Bordetella species and the role that Ser/Thr/Tyr phosphorylation may play in Bordetella biology and virulence.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Sandeep Kaur
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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28
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Halawa M, Cortleven A, Schmülling T, Heyl A. Characterization of CHARK, an unusual cytokinin receptor of rice. Sci Rep 2021; 11:1722. [PMID: 33462253 PMCID: PMC7814049 DOI: 10.1038/s41598-020-80223-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/21/2020] [Indexed: 11/14/2022] Open
Abstract
The signal transduction of the plant hormone cytokinin is mediated by a His-to-Asp phosphorelay. The canonical cytokinin receptor consists of an extra cytoplasmic hormone binding domain named cyclase/histidine kinase associated sensory extracellular (CHASE) and cytoplasmic histidine kinase and receiver domains. In addition to classical cytokinin receptors, a different type receptor—named CHASE domain receptor serine/threonine kinase (CHARK)—is also present in rice. It contains the same ligand binding domain as other cytokinin receptors but has a predicted Ser/Thr—instead of a His-kinase domain. Bioinformatic analysis indicates that CHARK is a retrogene and a product of trans-splicing. Here, we analyzed whether CHARK can function as a bona fide cytokinin receptor. A biochemical assay demonstrated its ability to bind cytokinin. Transient expression of CHARK in protoplasts increased their response to cytokinin. Expression of CHARK in an Arabidopsis receptor double mutant complemented its growth defects and restored the ability to activate cytokinin response genes, clearly demonstrating that CHARK functions as a cytokinin receptor. We propose that the CHARK gene presents an evolutionary novelty in the cytokinin signaling system.
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Affiliation(s)
- Mhyeddeen Halawa
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Anne Cortleven
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Thomas Schmülling
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany
| | - Alexander Heyl
- Institute of Biology/Applied Genetics, Dahlem Centre of Plant Science, Freie Universität Berlin, Albrecht-Thaer-Weg 6, 14195, Berlin, Germany. .,Biology Department, Adelphi University, 1 South Avenue, Garden City, NY, 11530-0701, USA.
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29
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Greco C, Catania R, Balacco DL, Taresco V, Musumeci F, Alexander C, Huett A, Schenone S. Synthesis and Antibacterial Evaluation of New Pyrazolo[3,4- d]pyrimidines Kinase Inhibitors. Molecules 2020; 25:molecules25225354. [PMID: 33207806 PMCID: PMC7696985 DOI: 10.3390/molecules25225354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/13/2022] Open
Abstract
Pyrazolo[3,4-d]pyrimidines represent an important class of heterocyclic compounds well-known for their anticancer activity exerted by the inhibition of eukaryotic protein kinases. Recently, pyrazolo[3,4-d]pyrimidines have become increasingly attractive for their potential antimicrobial properties. Here, we explored the activity of a library of in-house pyrazolo[3,4-d]pyrimidines, targeting human protein kinases, against Staphylococcus aureus and Escherichia coli and their interaction with ampicillin and kanamycin, representing important classes of clinically used antibiotics. Our results represent a first step towards the potential application of dual active pyrazolo[3,4-d]pyrimidine kinase inhibitors in the prevention and treatment of bacterial infections in cancer patients.
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Affiliation(s)
- Chiara Greco
- Dipartimento di Farmacia, Università di Genova, Viale Benedetto XV 3, 16132 Genova, Italy; (C.G.); (F.M.)
| | - Rosa Catania
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK;
| | - Dario Leonardo Balacco
- School of Dentistry, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B5 7EG, UK;
| | - Vincenzo Taresco
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK;
| | - Francesca Musumeci
- Dipartimento di Farmacia, Università di Genova, Viale Benedetto XV 3, 16132 Genova, Italy; (C.G.); (F.M.)
| | - Cameron Alexander
- School of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, UK;
| | - Alan Huett
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK;
- Correspondence: (A.H.); (S.S.)
| | - Silvia Schenone
- Dipartimento di Farmacia, Università di Genova, Viale Benedetto XV 3, 16132 Genova, Italy; (C.G.); (F.M.)
- Correspondence: (A.H.); (S.S.)
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30
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Poh WH, Lin J, Colley B, Müller N, Goh BC, Schleheck D, El Sahili A, Marquardt A, Liang Y, Kjelleberg S, Lescar J, Rice SA, Klebensberger J. The SiaABC threonine phosphorylation pathway controls biofilm formation in response to carbon availability in Pseudomonas aeruginosa. PLoS One 2020; 15:e0241019. [PMID: 33156827 PMCID: PMC7647112 DOI: 10.1371/journal.pone.0241019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/06/2020] [Indexed: 12/17/2022] Open
Abstract
The critical role of bacterial biofilms in chronic human infections calls for novel anti-biofilm strategies targeting the regulation of biofilm development. However, the regulation of biofilm development is very complex and can include multiple, highly interconnected signal transduction/response pathways, which are incompletely understood. We demonstrated previously that in the opportunistic, human pathogen P. aeruginosa, the PP2C-like protein phosphatase SiaA and the di-guanylate cyclase SiaD control the formation of macroscopic cellular aggregates, a type of suspended biofilms, in response to surfactant stress. In this study, we demonstrate that the SiaABC proteins represent a signal response pathway that functions through a partner switch mechanism to control biofilm formation. We also demonstrate that SiaABCD functionality is dependent on carbon substrate availability for a variety of substrates, and that upon carbon starvation, SiaB mutants show impaired dispersal, in particular with the primary fermentation product ethanol. This suggests that carbon availability is at least one of the key environmental cues integrated by the SiaABCD system. Further, our biochemical, physiological and crystallographic data reveals that the phosphatase SiaA and its kinase counterpart SiaB balance the phosphorylation status of their target protein SiaC at threonine 68 (T68). Crystallographic analysis of the SiaA-PP2C domain shows that SiaA is present as a dimer. Dynamic modelling of SiaA with SiaC suggested that SiaA interacts strongly with phosphorylated SiaC and dissociates rapidly upon dephosphorylation of SiaC. Further, we show that the known phosphatase inhibitor fumonisin inhibits SiaA mediated phosphatase activity in vitro. In conclusion, the present work improves our understanding of how P. aeuruginosa integrates specific environmental conditions, such as carbon availability and surfactant stress, to regulate cellular aggregation and biofilm formation. With the biochemical and structural characterization of SiaA, initial data on the catalytic inhibition of SiaA, and the interaction between SiaA and SiaC, our study identifies promising targets for the development of biofilm-interference drugs to combat infections of this aggressive opportunistic pathogen.
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Affiliation(s)
- Wee-Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jianqing Lin
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Brendan Colley
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicolai Müller
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Boon Chong Goh
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - David Schleheck
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Abbas El Sahili
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Andreas Marquardt
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Yang Liang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree Institute, The University of Technology Sydney, Sydney, Australia
| | - Janosch Klebensberger
- University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany
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31
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Ogura M. Glucose-Mediated Protein Arginine Phosphorylation/Dephosphorylation Regulates ylxR Encoding Nucleoid-Associated Protein and Cell Growth in Bacillus subtilis. Front Microbiol 2020; 11:590828. [PMID: 33101263 PMCID: PMC7546277 DOI: 10.3389/fmicb.2020.590828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/07/2020] [Indexed: 11/13/2022] Open
Abstract
Glucose is the most favorable carbon source for many bacteria, and these bacteria have several glucose-responsive networks. We proposed new glucose responsive system, which includes protein acetylation and probable translation control through TsaEBD, which is a tRNA modification enzyme required for the synthesis of threonylcarbamoyl adenosine (t6A)-tRNA. The system also includes nucleoid-associated protein YlxR, regulating more than 400 genes including many metabolic genes and the ylxR-containing operon driven by the PylxS promoter is induced by glucose. Thus, transposon mutagenesis was performed for searching regulatory factors for PylxS expression. As a result, ywlE was identified. The McsB kinase phosphorylates arginine (Arg) residues of proteins and the YwlE phosphatase counteracts against McsB through Arg-dephosphorylation. Phosphorylated Arg has been known to function as a tag for ClpCP-dependent protein degradation. The previous analysis identified TsaD as an Arg-phosphorylated protein. Our results showed that the McsB/YwlE system regulates PylxS expression through ClpCP-mediated protein degradation of TsaD. In addition, we observed that glucose induced ywlE expression and repressed mcsB expression. It was concluded that these phenomena would cause glucose induction (GI) of PylxS, based on the Western blot analyses of TsaD-FLAG. These observations and the previous those that many glycolytic enzymes are Arg-phosphorylated suggested that the McsB/YwlE system might be involved in cell growth in glucose-containing medium. We observed that the disruption of mcsB and ywlE resulted in an increase of cell mass and delayed growth, respectively, in semi-synthetic medium. These results provide us broader insights to the physiological roles of the McsB/YwlE system and protein Arg-phosphorylation.
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Affiliation(s)
- Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University, Shizuoka, Japan
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32
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Abo-Kadoum MA, Assad M, Dai Y, Lambert N, Moure UAE, Eltoukhy A, Nzaou SAE, Moaaz A, Xie J. Mycobacterium tuberculosis Raf kinase inhibitor protein (RKIP) Rv2140c is involved in cell wall arabinogalactan biosynthesis via phosphorylation. Microbiol Res 2020; 242:126615. [PMID: 33189070 DOI: 10.1016/j.micres.2020.126615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 09/19/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
Mycobacterium tuberculosis Rv2140c is a function unknown conserved phosphatidylethanolamine-binding protein (PEBP), homologous to Raf kinase inhibitor protein (RKIP) in human beings. To delineate its function, we heterologously expressed Rv2140c in a non-pathogenic M. smegmatis. Quantitative phosphoproteomic analysis between two recombinant strains Ms_Rv2140c and Ms_vec revealed that Rv2140c differentially regulate 425 phosphorylated sites representing 282 proteins. Gene ontology GO, and a cluster of orthologous groups COG analyses showed that regulated phosphoproteins by Rv2140c were mainly associated with metabolism and cellular processes. Rv2140c significantly repressed phosphoproteins involved in signaling, including serine/threonine-protein kinases and two-component system, and the arabinogalactan biosynthesis pathway phosphoproteins were markedly up-regulated, suggesting a role of Rv2140c in modulating cell wall. Consistent with phosphoproteomic data, Rv2140c altered some phenotypic properties of M. smegmatis such as colony morphology, cell wall permeability, survival in acidic conditions, and active lactose transport. In summary, we firstly demonstrated the role of PEBP protein Rv2140c, especially in phosphorylation of mycobacterial arabinogalactan biosynthesis proteins.
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Affiliation(s)
- M A Abo-Kadoum
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China; Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assuit Branch, Egypt
| | - Mohammed Assad
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Yongdong Dai
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Nzungize Lambert
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Ulrich Aymard Ekomi Moure
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Adel Eltoukhy
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assuit Branch, Egypt; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Stech A E Nzaou
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Asmaa Moaaz
- The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400716, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China.
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33
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Vallota-Eastman A, Arrington EC, Meeken S, Roux S, Dasari K, Rosen S, Miller JF, Valentine DL, Paul BG. Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria. BMC Genomics 2020; 21:664. [PMID: 32977771 PMCID: PMC7517822 DOI: 10.1186/s12864-020-07052-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. RESULTS Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. CONCLUSION We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.
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Affiliation(s)
- Alec Vallota-Eastman
- Interdepartmental Graduate Program for Marine Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Eleanor C Arrington
- Interdepartmental Graduate Program for Marine Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Siobhan Meeken
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA, 02543, USA
| | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Krishna Dasari
- Research Mentorship Program (RMP), University of California, Santa Barbara, CA, 93106, USA
| | - Sydney Rosen
- Research Mentorship Program (RMP), University of California, Santa Barbara, CA, 93106, USA
| | - Jeff F Miller
- Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - David L Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Blair G Paul
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA, 02543, USA.
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Xie Z, Zou Z, Raz A, Qin H, Fischetti V, Zhang S, Kreth J, Merritt J. Regulatory control of the Streptococcus mutans HdrRM LytTR Regulatory System functions via a membrane sequestration mechanism. Mol Microbiol 2020; 114:681-693. [PMID: 32706915 DOI: 10.1111/mmi.14576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 02/04/2023]
Abstract
Bacteria sense and respond to environmental changes via several broad categories of sensory signal transduction systems. Recently, we described the key features of a previously unrecognized, but widely conserved class of prokaryotic sensory system that we refer to as the LytTR Regulatory System (LRS). Our previous studies suggest that most, if not all, prokaryotic LRS membrane proteins serve as inhibitors of their cognate transcription regulators, but the inhibitory mechanisms employed have thus far remained a mystery. Using the Streptococcus mutans HdrRM LRS as a model, we demonstrate how the LRS membrane protein HdrM inhibits its cognate transcription regulator HdrR by tightly sequestering HdrR in a membrane-localized heteromeric HdrR/M complex. Membrane sequestration of HdrR prevents the positive feedback autoregulatory function of HdrR, thereby maintaining a low basal expression of the hdrRM operon. However, this mechanism can be antagonized by ectopically expressing a competitive inhibitor mutant form of HdrR that lacks its DNA binding ability while still retaining its HdrM interaction. Our results indicate that sequestration of HdrR is likely to be the only mechanism required to inhibit its transcription regulator function, suggesting that endogenous activation of the HdrRM LRS is probably achieved through a modulation of the HdrR/M interaction.
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Affiliation(s)
- Zhoujie Xie
- MOE Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhengzhong Zou
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, USA
| | - Assaf Raz
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA
| | - Hua Qin
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, USA
| | - Vincent Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, NY, USA
| | - Shan Zhang
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, USA
| | - Jens Kreth
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, USA
| | - Justin Merritt
- Department of Restorative Dentistry, Oregon Health and Science University, Portland, OR, USA.,Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
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Bonne Køhler J, Jers C, Senissar M, Shi L, Derouiche A, Mijakovic I. Importance of protein Ser/Thr/Tyr phosphorylation for bacterial pathogenesis. FEBS Lett 2020; 594:2339-2369. [PMID: 32337704 DOI: 10.1002/1873-3468.13797] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/16/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation regulates a large variety of biological processes in all living cells. In pathogenic bacteria, the study of serine, threonine, and tyrosine (Ser/Thr/Tyr) phosphorylation has shed light on the course of infectious diseases, from adherence to host cells to pathogen virulence, replication, and persistence. Mass spectrometry (MS)-based phosphoproteomics has provided global maps of Ser/Thr/Tyr phosphosites in bacterial pathogens. Despite recent developments, a quantitative and dynamic view of phosphorylation events that occur during bacterial pathogenesis is currently lacking. Temporal, spatial, and subpopulation resolution of phosphorylation data is required to identify key regulatory nodes underlying bacterial pathogenesis. Herein, we discuss how technological improvements in sample handling, MS instrumentation, data processing, and machine learning should improve bacterial phosphoproteomic datasets and the information extracted from them. Such information is expected to significantly extend the current knowledge of Ser/Thr/Tyr phosphorylation in pathogenic bacteria and should ultimately contribute to the design of novel strategies to combat bacterial infections.
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Affiliation(s)
- Julie Bonne Køhler
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Carsten Jers
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Mériem Senissar
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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36
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Wamp S, Rutter ZJ, Rismondo J, Jennings CE, Möller L, Lewis RJ, Halbedel S. PrkA controls peptidoglycan biosynthesis through the essential phosphorylation of ReoM. eLife 2020; 9:56048. [PMID: 32469310 PMCID: PMC7286690 DOI: 10.7554/elife.56048] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Peptidoglycan (PG) is the main component of bacterial cell walls and the target for many antibiotics. PG biosynthesis is tightly coordinated with cell wall growth and turnover, and many of these control activities depend upon PASTA-domain containing eukaryotic-like serine/threonine protein kinases (PASTA-eSTK) that sense PG fragments. However, only a few PG biosynthetic enzymes are direct kinase substrates. Here, we identify the conserved ReoM protein as a novel PASTA-eSTK substrate in the Gram-positive pathogen Listeria monocytogenes. Our data show that the phosphorylation of ReoM is essential as it controls ClpCP-dependent proteolytic degradation of the essential enzyme MurA, which catalyses the first committed step in PG biosynthesis. We also identify ReoY as a second novel factor required for degradation of ClpCP substrates. Collectively, our data imply that the first committed step of PG biosynthesis is activated through control of ClpCP protease activity in response to signals of PG homeostasis imbalance.
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Affiliation(s)
- Sabrina Wamp
- FG11 - Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
| | - Zoe J Rutter
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Jeanine Rismondo
- FG11 - Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany.,Department of General Microbiology, GZMB, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Claire E Jennings
- Newcastle Drug Discovery, Northern Institute for Cancer Research, Newcastle upon Tyne, United Kingdom
| | - Lars Möller
- ZBS 4 - Advanced Light and Electron Microscopy, Robert Koch Institute, Berlin, Germany
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Sven Halbedel
- FG11 - Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Wernigerode, Germany
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37
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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38
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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39
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Gong P, Lei P, Wang S, Zeng A, Lou H. Post-Translational Modifications Aid Archaeal Survival. Biomolecules 2020; 10:biom10040584. [PMID: 32290118 PMCID: PMC7226565 DOI: 10.3390/biom10040584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/22/2022] Open
Abstract
Since the pioneering work of Carl Woese, Archaea have fascinated biologists of almost all areas given their unique evolutionary status, wide distribution, high diversity, and ability to grow in special environments. Archaea often thrive in extreme conditions such as high temperature, high/low pH, high salinity, and anoxic ecosystems. All of these are threats to the stability and proper functioning of biological molecules, especially proteins and nucleic acids. Post-translational modifications (PTMs), such as phosphorylation, methylation, acetylation, and glycosylation, are reportedly widespread in Archaea and represent a critical adaptive mechanism to extreme habitats. Here, we summarize our current understanding of the contributions of PTMs to aid in extremophile survival, with a particular focus on the maintenance of genome stability.
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Affiliation(s)
- Ping Gong
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
- Correspondence: (P.G.); (H.L.)
| | - Ping Lei
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Shengping Wang
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Ao Zeng
- Hunan Institute of Microbiology, Changsha 410009, China; (P.L.); (S.W.); (A.Z.)
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology and Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Biological Sciences, China Agricultural University, No.2 Yuan-Ming-Yuan West Road, Beijing 100193, China
- Correspondence: (P.G.); (H.L.)
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40
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Rashid MM, Shatabda S, Hasan MM, Kurata H. Recent Development of Machine Learning Methods in Microbial Phosphorylation Sites. Curr Genomics 2020; 21:194-203. [PMID: 33071613 PMCID: PMC7521030 DOI: 10.2174/1389202921666200427210833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 01/10/2023] Open
Abstract
A variety of protein post-translational modifications has been identified that control many cellular functions. Phosphorylation studies in mycobacterial organisms have shown critical importance in diverse biological processes, such as intercellular communication and cell division. Recent technical advances in high-precision mass spectrometry have determined a large number of microbial phosphorylated proteins and phosphorylation sites throughout the proteome analysis. Identification of phosphorylated proteins with specific modified residues through experimentation is often labor-intensive, costly and time-consuming. All these limitations could be overcome through the application of machine learning (ML) approaches. However, only a limited number of computational phosphorylation site prediction tools have been developed so far. This work aims to present a complete survey of the existing ML-predictors for microbial phosphorylation. We cover a variety of important aspects for developing a successful predictor, including operating ML algorithms, feature selection methods, window size, and software utility. Initially, we review the currently available phosphorylation site databases of the microbiome, the state-of-the-art ML approaches, working principles, and their performances. Lastly, we discuss the limitations and future directions of the computational ML methods for the prediction of phosphorylation.
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Affiliation(s)
| | | | - Md. Mehedi Hasan
- Address correspondence to these authors at the Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Tel: +81-948-297-828;, E-mail: and Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Tel: +81-948-297-828; E-mail:
| | - Hiroyuki Kurata
- Address correspondence to these authors at the Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Tel: +81-948-297-828;, E-mail: and Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan; Tel: +81-948-297-828; E-mail:
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41
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Sámano-Sánchez H, Gibson TJ. Mimicry of Short Linear Motifs by Bacterial Pathogens: A Drugging Opportunity. Trends Biochem Sci 2020; 45:526-544. [PMID: 32413327 DOI: 10.1016/j.tibs.2020.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/25/2020] [Accepted: 03/03/2020] [Indexed: 12/11/2022]
Abstract
Bacterial pathogens have developed complex strategies to successfully survive and proliferate within their hosts. Throughout the infection cycle, direct interaction with host cells occurs. Many bacteria have been found to secrete proteins, such as effectors and toxins, directly into the host cell with the potential to interfere with cell regulatory processes, either enzymatically or through protein-protein interactions (PPIs). Short linear motifs (SLiMs) are abundant peptide modules in cell signaling proteins. Here, we cover the reported examples of eukaryotic-like SLiM mimicry being used by pathogenic bacteria to hijack host cell machinery and discuss how drugs targeting SLiM-regulated cell signaling networks are being evaluated for interference with bacterial infections. This emerging anti-infective opportunity may become an essential contributor to antibiotic replacement strategies.
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Affiliation(s)
- Hugo Sámano-Sánchez
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
| | - Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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42
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Rigo MM, Borges TJ, Lang BJ, Murshid A, Nitika, Wolfgeher D, Calderwood SK, Truman AW, Bonorino C. Host expression system modulates recombinant Hsp70 activity through post-translational modifications. FEBS J 2020; 287:10.1111/febs.15279. [PMID: 32144867 PMCID: PMC7483562 DOI: 10.1111/febs.15279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/22/2020] [Accepted: 03/03/2020] [Indexed: 12/17/2022]
Abstract
The use of model organisms for recombinant protein production results in the addition of model-specific post-translational modifications (PTMs) that can affect the structure, charge, and function of the protein. The 70-kDa heat shock proteins (Hsp70) were originally described as intracellular chaperones, with ATPase and foldase activity. More recently, new extracellular activities of Hsp70 proteins (e.g. as immunomodulators) have been identified. While some studies indicate an inflammatory potential for extracellular Hsp70 proteins, others suggest an immunosuppressive activity. We hypothesized that the production of recombinant Hsp70 in different expression systems would result in the addition of different PTMs, perhaps explaining at least some of these opposing immunological outcomes. We produced and purified Mycobacterium tuberculosis DnaK from two different systems, Escherichia coli and Pichia pastoris, and analyzed by mass spectrometry the protein preparations, investigating the impact of PTMs in an in silico and in vitro perspective. The comparisons of DnaK structures in silico highlighted that electrostatic and topographical differences exist that are dependent upon the expression system. Production of DnaK in the eukaryotic system dramatically affected its ATPase activity, and significantly altered its ability to downregulate MHC II and CD86 expression on murine dendritic cells (DCs). Phosphatase treatment of DnaK indicated that some of these differences related specifically to phosphorylation. Altogether, our data indicate that PTMs are an important characteristic of the expression system, with differences that impact interactions of Hsps with their ligands and subsequent functional activities.
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Affiliation(s)
- Mauricio M Rigo
- School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Av. Ipiranga, 6681, Porto Alegre Rio Grande do Sul, Zip Code: 90619-900, Brazil
| | - Thiago J Borges
- Schuster Family Transplantation Research Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA
| | - Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Ayesha Murshid
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, 28223
| | - Donald Wolfgeher
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave, Boston, MA, 02215, USA
| | - Andrew W Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, 28223
| | - Cristina Bonorino
- Laboratório de Imunoterapia, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite, 245, Porto Alegre Rio Grande do Sul, Zip Code: 90050-170, Brazil
- Department of Surgery, School of Medicine, University of California at San Diego, La Jolla, CA, 92037
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Dynamic Characterization of Protein and Posttranslational Modification Levels in Mycobacterial Cholesterol Catabolism. mSystems 2020; 5:5/1/e00424-19. [PMID: 31911463 PMCID: PMC6946793 DOI: 10.1128/msystems.00424-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cholesterol assimilation is a critical step in mycobacterial chronic infection. However, knowledge from the dynamic characterization of cholesterol metabolism in mycobacteria at the protein expression and PTM levels remains limited. Our study uncovered the landscape of protein expression, lysine acetylation, lysine propionylation, and S/T/Y phosphorylation during the metabolic changes from glucose to cholesterol in mycobacteria. The data showed that cholesterol-induced carbon shift resulted in the elevation of protein expression and lysine acylation in diverse metabolic enzymes involved in cholesterol degradation and that the presence of cholesterol also promoted the perturbations at the phosphorylation level in the kinase system in mycobacteria. This study systematically characterized the regulation of cholesterol catabolism at several different levels, which provided the detailed references in mycobacterial proteome and potential antimycobacterial strategies. Cholesterol of the host macrophage membrane is vital for mycobacterial infection, replication, and persistence. During chronic infection within host lung tissues, cholesterol facilitates the phagocytosis of mycobacteria into macrophages. Cholesterol degradation leads to increased flux of acetyl-coenzyme A (CoA) and propionyl-CoA, providing energy and building blocks for virulence macromolecules as well as donors for global protein acylation. Potential functions of lysine acylation are gradually revealed in bacterial survival and pathogenesis. However, the mycobacterial proteome and posttranslational modification (PTM) changes involved in the cholesterol catabolism bioprocess remain unclear. Here, we used nonpathogenic Mycobacterium smegmatis as a model and simultaneously monitored mycobacterial proteome and acetylome changes in the presence of glucose and cholesterol. We discovered that cholesterol metabolic enzymes were upregulated with respect to both protein expression levels and lysine acylation levels during the metabolic shift from glucose to cholesterol. After that, adenylating enzymes related to cholesterol metabolism were proven to be precisely regulated at the propionylation level by mycobacterial acyltransferase M. smegmatis Kat (MsKat) in response to cellular propionyl-CoA accumulation. Furthermore, the kinase expression and phosphorylation levels were also changed along with fluctuations in cholesterol levels. Our results expanded current knowledge of acylation regulation in the cholesterol catabolism of mycobacteria and provided references for possible antimycobacterium strategy. IMPORTANCE Cholesterol assimilation is a critical step in mycobacterial chronic infection. However, knowledge from the dynamic characterization of cholesterol metabolism in mycobacteria at the protein expression and PTM levels remains limited. Our study uncovered the landscape of protein expression, lysine acetylation, lysine propionylation, and S/T/Y phosphorylation during the metabolic changes from glucose to cholesterol in mycobacteria. The data showed that cholesterol-induced carbon shift resulted in the elevation of protein expression and lysine acylation in diverse metabolic enzymes involved in cholesterol degradation and that the presence of cholesterol also promoted the perturbations at the phosphorylation level in the kinase system in mycobacteria. This study systematically characterized the regulation of cholesterol catabolism at several different levels, which provided the detailed references in mycobacterial proteome and potential antimycobacterial strategies.
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Abstract
Reproduction in the bacterial kingdom predominantly occurs through binary fission-a process in which one parental cell is divided into two similarly sized daughter cells. How cell division, in conjunction with cell elongation and chromosome segregation, is orchestrated by a multitude of proteins has been an active area of research spanning the past few decades. Together, the monumental endeavors of multiple laboratories have identified several cell division and cell shape regulators as well as their underlying regulatory mechanisms in rod-shaped Escherichia coli and Bacillus subtilis, which serve as model organisms for Gram-negative and Gram-positive bacteria, respectively. Yet our understanding of bacterial cell division and morphology regulation is far from complete, especially in noncanonical and non-rod-shaped organisms. In this review, we focus on two proteins that are highly conserved in Gram-positive organisms, DivIVA and its homolog GpsB, and attempt to summarize the recent advances in this area of research and discuss their various roles in cell division, cell growth, and chromosome segregation in addition to their interactome and posttranslational regulation.
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Pelletier A, Freton C, Gallay C, Trouve J, Cluzel C, Franz-Wachtel M, Macek B, Jault JM, Grangeasse C, Guiral S. The Tyrosine-Autokinase UbK Is Required for Proper Cell Growth and Cell Morphology of Streptococcus pneumoniae. Front Microbiol 2019; 10:1942. [PMID: 31551943 PMCID: PMC6733980 DOI: 10.3389/fmicb.2019.01942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/07/2019] [Indexed: 12/11/2022] Open
Abstract
Protein phosphorylation is a key post-translational modification required for many cellular functions of the bacterial cell. Recently, we identified a new protein-kinase, named UbK, in Bacillus subtilis that belongs to a new family of protein-kinases widespread in bacteria. In this study, we analyze the function of UbK in Streptococcus pneumoniae. We show that UbK displays a tyrosine-kinase activity and autophosphorylates on a unique tyrosine in vivo. To get insights into its cellular role, we constructed a set of pneumococcal ubk mutants. Using conventional and electron microscopy, we show that the ubk deficient strain, as well as an ubk catalytic dead mutant, display both severe cell-growth and cell-morphology defects. The same defects are observed with a mutant mimicking permanent phosphorylation of UbK whereas they are not detected for a mutant mimicking defective autophosphorylation of UbK. Moreover, we find that UbK phosphorylation promotes its ability to hydrolyze ATP. These observations show that the hydrolysis of ATP by UbK serves not only for its autophosphorylation but also for a distinct purpose essential for the optimal cell growth and cell-morphogenesis of the pneumococcus. We thus propose a model in which the autophosphorylation/dephosphorylation of UbK regulates its cellular function through a negative feedback loop.
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Affiliation(s)
- Anaïs Pelletier
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Clément Gallay
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Jennyfer Trouve
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Caroline Cluzel
- Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, UMR 5305 CNRS/Université Lyon 1, Lyon, France
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Jean-Michel Jault
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
| | - Sébastien Guiral
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS/Université Lyon 1, Lyon, France
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The Ser/Thr Kinase PrkC Participates in Cell Wall Homeostasis and Antimicrobial Resistance in Clostridium difficile. Infect Immun 2019; 87:IAI.00005-19. [PMID: 31085703 DOI: 10.1128/iai.00005-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/26/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridium difficile is the leading cause of antibiotic-associated diarrhea in adults. During infection, C. difficile must detect the host environment and induce an appropriate survival strategy. Signal transduction networks involving serine/threonine kinases (STKs) play key roles in adaptation, as they regulate numerous physiological processes. PrkC of C. difficile is an STK with two PASTA domains. We showed that PrkC is membrane associated and is found at the septum. We observed that deletion of prkC affects cell morphology with an increase in mean size, cell length heterogeneity, and presence of abnormal septa. A ΔprkC mutant was able to sporulate and germinate but was less motile and formed more biofilm than the wild-type strain. Moreover, a ΔprkC mutant was more sensitive to antimicrobial compounds that target the cell envelope, such as the secondary bile salt deoxycholate, cephalosporins, cationic antimicrobial peptides, and lysozyme. This increased susceptibility was not associated with differences in peptidoglycan or polysaccharide II composition. However, the ΔprkC mutant had less peptidoglycan and released more polysaccharide II into the supernatant. A proteomic analysis showed that the majority of C. difficile proteins associated with the cell wall were less abundant in the ΔprkC mutant than the wild-type strain. Finally, in a hamster model of infection, the ΔprkC mutant had a colonization delay that did not significantly affect overall virulence.
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Abstract
Bacterial pathogens can switch signaling by sensing threonine phosphorylation. In this issue of Structure, Heinkel et al. (2018) report novel rearrangements linking threonine phosphorylation to tandem forkhead-associated (FHA) domains from an ATP-binding cassette (ABC) transporter. The resulting associations probably regulate oligomerization and transport in Mycoplasma tuberculosis.
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Affiliation(s)
- Steven R Van Doren
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, MO 65211, USA.
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Bellinzoni M, Wehenkel AM, Durán R, Alzari PM. Novel mechanistic insights into physiological signaling pathways mediated by mycobacterial Ser/Thr protein kinases. Microbes Infect 2019; 21:222-229. [PMID: 31254628 DOI: 10.1016/j.micinf.2019.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022]
Abstract
Protein phosphorylation is known to be one of the keystones of signal sensing and transduction in all living organisms. Once thought to be essentially confined to the eukaryotic kingdoms, reversible phosphorylation on serine, threonine and tyrosine residues, has now been shown to play a major role in many prokaryotes, where the number of Ser/Thr protein kinases (STPKs) equals or even exceeds that of two component systems. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is one of the most studied organisms for the role of STPK-mediated signaling in bacteria. Driven by the interest and tractability of these enzymes as potential therapeutic targets, extensive studies revealed the remarkable conservation of protein kinases and their cognate phosphatases across evolution, and their involvement in bacterial physiology and virulence. Here, we present an overview of the current knowledge of mycobacterial STPKs structures and kinase activation mechanisms, and we then focus on PknB and PknG, two well-characterized STPKs that are essential for the intracellular survival of the bacillus. We summarize the mechanistic evidence that links PknB to the regulation of peptidoglycan synthesis in cell division and morphogenesis, and the major findings that establishes PknG as a master regulator of central carbon and nitrogen metabolism. Two decades after the discovery of STPKs in M. tuberculosis, the emerging landscape of O-phosphosignaling is starting to unveil how eukaryotic-like kinases can be engaged in unique, non-eukaryotic-like, signaling mechanisms in mycobacteria.
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Affiliation(s)
- Marco Bellinzoni
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Anne Marie Wehenkel
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Rosario Durán
- Unidad de Bioquímica y Proteómica Analíticas, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Mataojo 2020, Montevideo 11400, Uruguay
| | - Pedro M Alzari
- Unit of Structural Microbiology, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528 & Université Paris Diderot, 25 rue du Docteur Roux, 75724 Paris cedex 15, France.
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49
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Abstract
Bacterial spores can remain dormant for years but possess the remarkable ability to germinate, within minutes, once nutrients become available. However, it still remains elusive how such instant awakening of cellular machineries is achieved. Utilizing Bacillus subtilis as a model, we show that YwlE arginine (Arg) phosphatase is crucial for spore germination. Accordingly, the absence of the Arg kinase McsB accelerated the process. Arg phosphoproteome of dormant spores uncovered a unique set of Arg-phosphorylated proteins involved in key biological functions, including translation and transcription. Consequently, we demonstrate that during germination, YwlE dephosphorylates an Arg site on the ribosome-associated chaperone Tig, enabling its association with the ribosome to reestablish translation. Moreover, we show that Arg dephosphorylation of the housekeeping σ factor A (SigA), mediated by YwlE, facilitates germination by activating the transcriptional machinery. Subsequently, we reveal that transcription is reinitiated at the onset of germination and its recommencement precedes that of translation. Thus, Arg dephosphorylation elicits the most critical stages of spore molecular resumption, placing this unusual post-translational modification as a major regulator of a developmental process in bacteria.
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Lipa P, Vinardell JM, Janczarek M. Transcriptomic Studies Reveal that the Rhizobium leguminosarum Serine/Threonine Protein Phosphatase PssZ has a Role in the Synthesis of Cell-Surface Components, Nutrient Utilization, and Other Cellular Processes. Int J Mol Sci 2019; 20:ijms20122905. [PMID: 31197117 PMCID: PMC6628131 DOI: 10.3390/ijms20122905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023] Open
Abstract
Rhizobium leguminosarum bv. trifolii is a soil bacterium capable of establishing symbiotic associations with clover plants (Trifolium spp.). Surface polysaccharides, transport systems, and extracellular components synthesized by this bacterium are required for both the adaptation to changing environmental conditions and successful infection of host plant roots. The pssZ gene located in the Pss-I region, which is involved in the synthesis of extracellular polysaccharide, encodes a protein belonging to the group of serine/threonine protein phosphatases. In this study, a comparative transcriptomic analysis of R. leguminosarum bv. trifolii wild-type strain Rt24.2 and its derivative Rt297 carrying a pssZ mutation was performed. RNA-Seq data identified a large number of genes differentially expressed in these two backgrounds. Transcriptome profiling of the pssZ mutant revealed a role of the PssZ protein in several cellular processes, including cell signalling, transcription regulation, synthesis of cell-surface polysaccharides and components, and bacterial metabolism. In addition, we show that inactivation of pssZ affects the rhizobial ability to grow in the presence of different sugars and at various temperatures, as well as the production of different surface polysaccharides. In conclusion, our results identified a set of genes whose expression was affected by PssZ and confirmed the important role of this protein in the rhizobial regulatory network.
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Affiliation(s)
- Paulina Lipa
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
| | - José-María Vinardell
- Department of Microbiology, Faculty of Biology, University of Sevilla, Avda. Reina Mercedes 6, 41012 Sevilla, Spain.
| | - Monika Janczarek
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19 St., 20-033 Lublin, Poland.
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