1
|
Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn P, Hanefeld U. Methyltransferases: Functions and Applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state-of-the-art of S-adenosylmethionine (SAM)-dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O-, N-, C- and S-MTs, their synthetic applications and potential for compound diversification is given.
Collapse
Affiliation(s)
- Eman Abdelraheem
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
| | - Benjamin Thair
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - Romina Fernández Varela
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Emely Jockmann
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Désirée Popadić
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Helen C. Hailes
- Department of ChemistryUniversity College London20 Gordon StreetLondonWC1H 0AJUK
| | - John M. Ward
- Department of Biochemical EngineeringBernard Katz BuildingUniversity College LondonLondonWC1E 6BTUK
| | - Adolfo M. Iribarren
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Elizabeth S. Lewkowicz
- Laboratorio de Biotransformaciones y Química de Ácidos NucleicosUniversidad Nacional de QuilmesRoque S. Peña 352B1876BXDBernalArgentina
| | - Jennifer N. Andexer
- Institute of Pharmaceutical SciencesUniversity of FreiburgAlbertstr. 2579104FreiburgGermany
| | - Peter‐Leon Hagedoorn
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
| | - Ulf Hanefeld
- BiocatalysisDepartment of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelft (TheNetherlands
| |
Collapse
|
2
|
Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [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: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
Collapse
Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| |
Collapse
|
3
|
Recent structural insights into bacterial microcompartment shells. Curr Opin Microbiol 2021; 62:51-60. [PMID: 34058518 DOI: 10.1016/j.mib.2021.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/26/2021] [Accepted: 04/20/2021] [Indexed: 02/05/2023]
Abstract
Bacterial microcompartments are organelle-like structures that enhance a variety of metabolic functions in diverse bacteria. Composed entirely of proteins, thousands of homologous hexameric shell proteins tesselate to form facets while pentameric proteins form the vertices of a polyhedral shell that encapsulates various enzymes, substrates and cofactors. Recent structural data have highlighted nuanced variations in the sequence and topology of microcompartment shell proteins, emphasizing how variation and specialization enable the construction of complex molecular machines. Recent studies engineering synthetic miniaturized microcompartment shells provide additional frameworks for dissecting principles of microcompartment structure and assembly. This review updates our current understanding of bacterial microcompartment shell proteins, providing new insights and highlighting outstanding questions.
Collapse
|
4
|
Garcia-Alles LF, Root K, Maveyraud L, Aubry N, Lesniewska E, Mourey L, Zenobi R, Truan G. Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components. PLoS One 2019; 14:e0223877. [PMID: 31603944 PMCID: PMC6788708 DOI: 10.1371/journal.pone.0223877] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
The carboxysome is a bacterial micro-compartment (BMC) subtype that encapsulates enzymatic activities necessary for carbon fixation. Carboxysome shells are composed of a relatively complex cocktail of proteins, their precise number and identity being species dependent. Shell components can be classified in two structural families, the most abundant class associating as hexamers (BMC-H) that are supposed to be major players for regulating shell permeability. Up to recently, these proteins were proposed to associate as homo-oligomers. Genomic data, however, demonstrated the existence of paralogs coding for multiple shell subunits. Here, we studied cross-association compatibilities among BMC-H CcmK proteins of Synechocystis sp. PCC6803. Co-expression in Escherichia coli proved a consistent formation of hetero-hexamers combining CcmK1 and CcmK2 or, remarkably, CcmK3 and CcmK4 subunits. Unlike CcmK1/K2 hetero-hexamers, the stoichiometry of incorporation of CcmK3 in associations with CcmK4 was low. Cross-interactions implicating other combinations were weak, highlighting a structural segregation of the two groups that could relate to gene organization. Sequence analysis and structural models permitted the localization of interactions that would favor formation of CcmK3/K4 hetero-hexamers. The crystallization of these CcmK3/K4 associations conducted to the elucidation of a structure corresponding to the CcmK4 homo-hexamer. Yet, subunit exchange could not be demonstrated in vitro. Biophysical measurements showed that hetero-hexamers are thermally less stable than homo-hexamers, and impeded in forming larger assemblies. These novel findings are discussed within the context of reported data to propose a functional scenario in which minor CcmK3/K4 incorporation in shells would introduce sufficient local disorder as to allow shell remodeling necessary to adapt rapidly to environmental changes.
Collapse
Affiliation(s)
- Luis F. Garcia-Alles
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Laurent Maveyraud
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nathalie Aubry
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Lionel Mourey
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Gilles Truan
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| |
Collapse
|
5
|
Abstract
Ethanolamine (EA) is a valuable source of carbon and/or nitrogen for bacteria capable of its catabolism. Because it is derived from the membrane phospholipid phosphatidylethanolamine, it is particularly prevalent in the gastrointestinal tract, which is membrane rich due to turnover of the intestinal epithelium and the resident microbiota. Intriguingly, many gut pathogens carry the eut (ethanolamine utilization) genes. EA utilization has been studied for about 50 years, with most of the early work occurring in just a couple of species of Enterobacteriaceae. Once the metabolic pathways and enzymes were characterized by biochemical approaches, genetic screens were used to map the various activities to the eut genes. With the rise of genomics, the diversity of bacteria containing the eut genes and surprising differences in eut gene content were recognized. Some species contain nearly 20 genes and encode many accessory proteins, while others contain only the core catabolic enzyme. Moreover, the eut genes are regulated by very different mechanisms, depending on the organism and the eut regulator encoded. In the last several years, exciting progress has been made in elucidating the complex regulatory mechanisms that govern eut gene expression. Furthermore, a new appreciation for how EA contributes to infection and colonization in the host is emerging. In addition to providing an overview of EA-related biology, this minireview will give special attention to these recent advances.
Collapse
|
6
|
Garcia-Alles LF, Lesniewska E, Root K, Aubry N, Pocholle N, Mendoza CI, Bourillot E, Barylyuk K, Pompon D, Zenobi R, Reguera D, Truan G. Spontaneous non-canonical assembly of CcmK hexameric components from β-carboxysome shells of cyanobacteria. PLoS One 2017; 12:e0185109. [PMID: 28934279 PMCID: PMC5608322 DOI: 10.1371/journal.pone.0185109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023] Open
Abstract
CcmK proteins are major constituents of icosahedral shells of β-carboxysomes, a bacterial microcompartment that plays a key role for CO2 fixation in nature. Supported by the characterization of bidimensional (2D) layers of packed CcmK hexamers in crystal and electron microscopy structures, CcmK are assumed to be the major components of icosahedral flat facets. Here, we reassessed the validity of this model by studying CcmK isoforms from Synechocystis sp. PCC6803. Native mass spectrometry studies confirmed that CcmK are hexamers in solution. Interestingly, potential pre-assembled intermediates were also detected with CcmK2. Atomic-force microscopy (AFM) imaging under quasi-physiological conditions confirmed the formation of canonical flat sheets with CcmK4. Conversely, CcmK2 formed both canonical and striped-patterned patches, while CcmK1 assembled into remarkable supra-hexameric curved honeycomb-like mosaics. Mutational studies ascribed the propensity of CcmK1 to form round assemblies to a combination of two features shared by at least one CcmK isoform in most β-cyanobacteria: a displacement of an α helical portion towards the hexamer edge, where a potential phosphate binding funnel forms between packed hexamers, and the presence of a short C-terminal extension in CcmK1. All-atom molecular dynamics supported a contribution of phosphate molecules sandwiched between hexamers to bend CcmK1 assemblies. Formation of supra-hexameric curved structures could be reproduced in coarse-grained simulations, provided that adhesion forces to the support were weak. Apart from uncovering unprecedented CcmK self-assembly features, our data suggest the possibility that transitions between curved and flat assemblies, following cargo maturation, could be important for the biogenesis of β-carboxysomes, possibly also of other BMC.
Collapse
Affiliation(s)
- Luis F. Garcia-Alles
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
- * E-mail: (LFGA); (GT)
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Nathalie Aubry
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
| | - Nicolas Pocholle
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Carlos I. Mendoza
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Cd Mx, México
| | - Eric Bourillot
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Denis Pompon
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - David Reguera
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
| | - Gilles Truan
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
- * E-mail: (LFGA); (GT)
| |
Collapse
|
7
|
Kwon DH, Kim S, Jung YO, Roh KH, Kim L, Kim BW, Hong SB, Lee IY, Song JH, Lee WC, Choi EJ, Hwang KY, Song HK. The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane. Autophagy 2016; 13:70-81. [PMID: 27791457 DOI: 10.1080/15548627.2016.1243199] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Hosts utilize macroautophagy/autophagy to clear invading bacteria; however, bacteria have also developed a specific mechanism to survive by manipulating the host cell autophagy mechanism. One pathogen, Legionella pneumophila, can hinder host cell autophagy by using the specific effector protein RavZ that cleaves phosphatidylethanolamine-conjugated LC3 on the phagophore membrane. However, the detailed molecular mechanisms associated with the function of RavZ have hitherto remained unclear. Here, we report on the biochemical characteristics of the RavZ-LC3 interaction, the solution structure of the 1:2 complex between RavZ and LC3, and crystal structures of RavZ showing different conformations of the active site loop without LC3. Based on our biochemical, structural, and cell-based analyses of RavZ and LC3, both distant flexible N- and C-terminal regions containing LC3-interacting region (LIR) motifs are important for substrate recognition. These results suggest a novel mechanism of RavZ action on the phagophore membrane and lay the groundwork for understanding how bacterial pathogens can survive autophagy.
Collapse
Affiliation(s)
- Do Hoon Kwon
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Sulhee Kim
- b Division of Biotechnology, Korea University , Seongbuk-gu, Seoul , Korea
| | - Yang Ouk Jung
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Kyung-Hye Roh
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Leehyeon Kim
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Byeong-Won Kim
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Seung Beom Hong
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - In Young Lee
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Ju Han Song
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Woo Cheol Lee
- b Division of Biotechnology, Korea University , Seongbuk-gu, Seoul , Korea
| | - Eui-Ju Choi
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| | - Kwang Yeon Hwang
- b Division of Biotechnology, Korea University , Seongbuk-gu, Seoul , Korea
| | - Hyun Kyu Song
- a Department of Life Sciences , Korea University , Seongbuk-gu, Seoul , Korea
| |
Collapse
|
8
|
Bobik TA, Lehman BP, Yeates TO. Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways. Mol Microbiol 2015; 98:193-207. [PMID: 26148529 PMCID: PMC4718714 DOI: 10.1111/mmi.13117] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2015] [Indexed: 12/15/2022]
Abstract
Prokaryotes use subcellular compartments for a variety of purposes. An intriguing example is a family of complex subcellular organelles known as bacterial microcompartments (MCPs). MCPs are widely distributed among bacteria and impact processes ranging from global carbon fixation to enteric pathogenesis. Overall, MCPs consist of metabolic enzymes encased within a protein shell, and their function is to optimize biochemical pathways by confining toxic or volatile metabolic intermediates. MCPs are fundamentally different from other organelles in having a complex protein shell rather than a lipid-based membrane as an outer barrier. This unusual feature raises basic questions about organelle assembly, protein targeting and metabolite transport. In this review, we discuss the three best-studied MCPs highlighting atomic-level models for shell assembly, targeting sequences that direct enzyme encapsulation, multivalent proteins that organize the lumen enzymes, the principles of metabolite movement across the shell, internal cofactor recycling, a potential system of allosteric regulation of metabolite transport and the mechanism and rationale behind the functional diversification of the proteins that form the shell. We also touch on some potential biotechnology applications of an unusual compartment designed by nature to optimize metabolic processes within a cellular context.
Collapse
Affiliation(s)
- Thomas A. Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Brent P. Lehman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| |
Collapse
|
9
|
Role and Function of LitR, an Adenosyl B12-Bound Light-Sensitive Regulator of Bacillus megaterium QM B1551, in Regulation of Carotenoid Production. J Bacteriol 2015; 197:2301-15. [PMID: 25917914 DOI: 10.1128/jb.02528-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/23/2015] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED The LitR/CarH family of proteins is a light-sensitive MerR family of transcriptional regulators that contain an adenosyl B12 (coenzyme B12 or AdoB12)-binding domain at the C terminus. The genes encoding these proteins are found in phylogenetically diverse bacterial genera; however, the biochemical properties of these proteins from Gram-positive bacteria remain poorly understood. We performed genetic and biochemical analyses of a homolog of the LitR protein from Bacillus megaterium QM B1551, a Gram-positive endospore-forming soil bacterium. Carotenoid production was induced by illumination in this bacterium. In vivo analysis demonstrated that LitR plays a central role in light-inducible carotenoid production and serves as a negative regulator of the light-inducible transcription of crt and litR itself. Biochemical evidence showed that LitR in complex with AdoB12 binds to the promoter regions of litR and the crt operon in a light-sensitive manner. In vitro transcription experiments demonstrated that AdoB12-LitR inhibited the specific transcription of the crt promoter generated by a σ(A)-containing RNA polymerase holoenzyme under dark conditions. Collectively, these data indicate that the AdoB12-LitR complex serves as a photoreceptor with DNA-binding activity in B. megaterium QM B1551 and that its function as a transcriptional repressor is fundamental to the light-induced carotenoid production. IMPORTANCE Members of the LitR/CarH family are AdoB12-based photosensors involved in light-inducible carotenoid production in nonphototrophic Gram-negative bacteria. Our study revealed that Bacillus LitR in complex with AdoB12 also serves as a transcriptional regulator with a photosensory function, which indicates that the LitR/CarH family is generally involved in the light-inducible carotenoid production of nonphototrophic bacteria.
Collapse
|
10
|
Abstract
Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.
Collapse
|
11
|
Förster A, Planamente S, Manoli E, Lossi NS, Freemont PS, Filloux A. Coevolution of the ATPase ClpV, the sheath proteins TssB and TssC, and the accessory protein TagJ/HsiE1 distinguishes type VI secretion classes. J Biol Chem 2014; 289:33032-43. [PMID: 25305017 PMCID: PMC4239648 DOI: 10.1074/jbc.m114.600510] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The type VI secretion system (T6SS) is a bacterial nanomachine for the transport of effector molecules into prokaryotic and eukaryotic cells. It involves the assembly of a tubular structure composed of TssB and TssC that is similar to the tail sheath of bacteriophages. The sheath contracts to provide the energy needed for effector delivery. The AAA+ ATPase ClpV disassembles the contracted sheath, which resets the systems for reassembly of an extended sheath that is ready to fire again. This mechanism is crucial for T6SS function. In Vibrio cholerae, ClpV binds the N terminus of TssC within a hydrophobic groove. In this study, we resolved the crystal structure of the N-terminal domain of Pseudomonas aeruginosa ClpV1 and observed structural alterations in the hydrophobic groove. The modification in the ClpV1 groove is matched by a change in the N terminus of TssC, suggesting the existence of distinct T6SS classes. An accessory T6SS component, TagJ/HsiE, exists predominantly in one of the classes. Using bacterial two-hybrid approaches, we showed that the P. aeruginosa homolog HsiE1 interacts strongly with ClpV1. We then resolved the crystal structure of HsiE1 in complex with the N terminus of HsiB1, a TssB homolog and component of the contractile sheath. Phylogenetic analysis confirmed that these differences distinguish T6SS classes that resulted from a functional co-evolution between TssB, TssC, TagJ/HsiE, and ClpV. The interaction of TagJ/HsiE with the sheath as well as with ClpV suggests an alternative mode of disassembly in which HsiE recruits the ATPase to the sheath.
Collapse
Affiliation(s)
| | - Sara Planamente
- the Medical Research Council Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Eleni Manoli
- the Medical Research Council Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Nadine S Lossi
- the Medical Research Council Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Alain Filloux
- the Medical Research Council Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|
12
|
Keeling TJ, Samborska B, Demers RW, Kimber MS. Interactions and structural variability of β-carboxysomal shell protein CcmL. PHOTOSYNTHESIS RESEARCH 2014; 121:125-133. [PMID: 24504539 DOI: 10.1007/s11120-014-9973-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/14/2014] [Indexed: 06/03/2023]
Abstract
CcmL is a small, pentameric protein that is argued to fill the vertices of β-carboxysomal shell. Here we report the structures of two CcmL orthologs, those from Nostoc sp. PCC 7120 and Thermosynechococcus elongatus BP-1. These structures broadly resemble those previously reported for other strains. However, the Nostoc CcmL structure shows an interesting pattern of behavior where two loops that map to the base of the pentamer adopt either an out or in conformation, with a consistent (over six pentamers) out-in-out-in-in pattern of protomers. The pentamers in this structure are also consistently organized into a back-to-back decamer, though evidence suggests that this is likely not present in solution. Förster resonance energy transfer experiments were able to show a weak interaction between CcmL and CcmK2 when CcmK2 was present at >100 μM. Since CcmK2 forms defined bodies with approximately 200 nm diameter at this concentration, this would support the idea that CcmL can only interact with CcmK2 at rare defect points in the growing shell.
Collapse
Affiliation(s)
- Thomas J Keeling
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | | | | |
Collapse
|
13
|
Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA. Diverse bacterial microcompartment organelles. Microbiol Mol Biol Rev 2014. [PMID: 25184561 DOI: 10.1128/mmbr.00009–14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.
Collapse
Affiliation(s)
- Chiranjit Chowdhury
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Sharmistha Sinha
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Sunny Chun
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Todd O Yeates
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| |
Collapse
|
14
|
Kimura S, Miyauchi K, Ikeuchi Y, Thiaville PC, Crécy-Lagard VD, Suzuki T. Discovery of the β-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs. Nucleic Acids Res 2014; 42:9350-65. [PMID: 25063302 PMCID: PMC4132733 DOI: 10.1093/nar/gku618] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Methylation is a versatile reaction involved in the synthesis and modification of biologically active molecules, including RNAs. N(6)-methyl-threonylcarbamoyl adenosine (m(6)t(6)A) is a post-transcriptional modification found at position 37 of tRNAs from bacteria, insect, plants, and mammals. Here, we report that in Escherichia coli, yaeB (renamed as trmO) encodes a tRNA methyltransferase responsible for the N(6)-methyl group of m(6)t(6)A in tRNA(Thr) specific for ACY codons. TrmO has a unique single-sheeted β-barrel structure and does not belong to any known classes of methyltransferases. Recombinant TrmO employs S-adenosyl-L-methionine (AdoMet) as a methyl donor to methylate t(6)A to form m(6)t(6)A in tRNA(Thr). Therefore, TrmO/YaeB represents a novel category of AdoMet-dependent methyltransferase (Class VIII). In a ΔtrmO strain, m(6)t(6)A was converted to cyclic t(6)A (ct(6)A), suggesting that t(6)A is a common precursor for both m(6)t(6)A and ct(6)A. Furthermore, N(6)-methylation of t(6)A enhanced the attenuation activity of the thr operon, suggesting that TrmO ensures efficient decoding of ACY. We also identified a human homolog, TRMO, indicating that m(6)t(6)A plays a general role in fine-tuning of decoding in organisms from bacteria to mammals.
Collapse
Affiliation(s)
- Satoshi Kimura
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kenjyo Miyauchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoshiho Ikeuchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Patrick C Thiaville
- Genetics and Genomics Graduate Program University of Florida Genetics Institute Department of Microbiology, University of Florida, Gainesville, Florida 32611-0700, USA Institut de Génétique et Microbiologie, Université of Paris-Sud, Orsay, France
| | - Valérie de Crécy-Lagard
- University of Florida Genetics Institute Department of Microbiology, University of Florida, Gainesville, Florida 32611-0700, USA
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
15
|
Zhao S, Sakai A, Zhang X, Vetting MW, Kumar R, Hillerich B, San Francisco B, Solbiati J, Steves A, Brown S, Akiva E, Barber A, Seidel RD, Babbitt PC, Almo SC, Gerlt JA, Jacobson MP. Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks. eLife 2014; 3. [PMID: 24980702 PMCID: PMC4113996 DOI: 10.7554/elife.03275] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/26/2014] [Indexed: 01/10/2023] Open
Abstract
Metabolic pathways in eubacteria and archaea often are encoded by operons and/or gene clusters (genome neighborhoods) that provide important clues for assignment of both enzyme functions and metabolic pathways. We describe a bioinformatic approach (genome neighborhood network; GNN) that enables large scale prediction of the in vitro enzymatic activities and in vivo physiological functions (metabolic pathways) of uncharacterized enzymes in protein families. We demonstrate the utility of the GNN approach by predicting in vitro activities and in vivo functions in the proline racemase superfamily (PRS; InterPro IPR008794). The predictions were verified by measuring in vitro activities for 51 proteins in 12 families in the PRS that represent ∼85% of the sequences; in vitro activities of pathway enzymes, carbon/nitrogen source phenotypes, and/or transcriptomic studies confirmed the predicted pathways. The synergistic use of sequence similarity networks3 and GNNs will facilitate the discovery of the components of novel, uncharacterized metabolic pathways in sequenced genomes. DOI:http://dx.doi.org/10.7554/eLife.03275.001 DNA molecules are polymers in which four nucleotides—guanine, adenine, thymine, and cytosine—are arranged along a sugar backbone. The sequence of these four nucleotides along the DNA strand determines the genetic code of the organism, and can be deciphered using various genome sequencing techniques. Microbial genomes are particularly easy to sequence as they contain fewer than several million nucleotides, compared with the 3 billion or so nucleotides that are present in the human genome. Reading a genome sequence is straight forward, but predicting the physiological functions of the proteins encoded by the genes in the sequence can be challenging. In a process called genome annotation, the function of protein is predicted by comparing the relevant gene to the genes of proteins with known functions. However, microbial genomes and proteins are hugely diverse and over 50% of the microbial genomes that have been sequenced have not yet been related to any physiological function. With thousands of microbial genomes waiting to be deciphered, large scale approaches are needed. Zhao et al. take advantage of a particular characteristic of microbial genomes. DNA sequences that code for two proteins required for the same task tend to be closer to each other in the genome than two sequences that code for unrelated functions. Operons are an extreme example; an operon is a unit of DNA that contains several genes that are expressed as proteins at the same time. Zhao et al. have developed a bioinformatic method called the genome neighbourhood network approach to work out the function of proteins based on their position relative to other proteins in the genome. When applied to the proline racemase superfamily (PRS), which contains enzymes with similar sequences that can catalyze three distinct chemical reactions, the new approach was able to assign a function to the majority of proteins in a public database of PRS enzymes, and also revealed new members of the PRS family. Experiments confirmed that the proteins behaved as predicted. The next challenge is to develop the genome neighbourhood network approach so that it can be applied to more complex systems. DOI:http://dx.doi.org/10.7554/eLife.03275.002
Collapse
Affiliation(s)
- Suwen Zhao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| | - Ayano Sakai
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Xinshuai Zhang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, New York, United States
| | - Ritesh Kumar
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Brandan Hillerich
- Department of Biochemistry, Albert Einstein College of Medicine, New York, United States
| | - Brian San Francisco
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Jose Solbiati
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Adam Steves
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Shoshana Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Alan Barber
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Ronald D Seidel
- Department of Biochemistry, Albert Einstein College of Medicine, New York, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, New York, United States
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
16
|
Sutter M, Wilson SC, Deutsch S, Kerfeld CA. Two new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species. PHOTOSYNTHESIS RESEARCH 2013; 118:9-16. [PMID: 23949415 DOI: 10.1007/s11120-013-9909-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 08/01/2013] [Indexed: 06/02/2023]
Abstract
Cyanobacteria have evolved a unique carbon fixation organelle known as the carboxysome that compartmentalizes the enzymes RuBisCO and carbonic anhydrase. This effectively increases the local CO2 concentration at the active site of RuBisCO and decreases its relatively unproductive side reaction with oxygen. Carboxysomes consist of a protein shell composed of hexameric and pentameric proteins arranged in icosahedral symmetry. Facets composed of hexameric proteins are connected at the vertices by pentameric proteins. Structurally homologous pentamers and hexamers are also found in heterotrophic bacteria where they form architecturally related microcompartments such as the Eut and Pdu organelles for the metabolism of ethanolamine and propanediol, respectively. Here we describe two new high-resolution structures of the pentameric shell protein CcmL from the cyanobacteria Thermosynechococcus elongatus and Gloeobacter violaceus and provide detailed analysis of their characteristics and comparison with related shell proteins.
Collapse
Affiliation(s)
- Markus Sutter
- United States Department of Energy - Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | | | | | | |
Collapse
|
17
|
Kim EY, Tullman-Ercek D. Engineering nanoscale protein compartments for synthetic organelles. Curr Opin Biotechnol 2012; 24:627-32. [PMID: 23273660 DOI: 10.1016/j.copbio.2012.11.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/12/2012] [Accepted: 11/29/2012] [Indexed: 01/05/2023]
Abstract
Advances in metabolic engineering have given rise to the biological production of novel fuels and chemicals, but yields are often low without significant optimization. One generalizable solution is to create a specialized organelle for the sequestration of engineered metabolic pathways. Bacterial microcompartments are an excellent scaffold for such an organelle. These compartments consist of a porous protein shell that encapsulates enzymes. To repurpose these structures, researchers have begun to determine how the protein shell is assembled, how pores may be used to control small molecule transport across the protein shell, and how to target heterologous enzymes to the compartment interior. With these advances, it will soon be possible to use engineered forms of these protein shells to create designer organelles.
Collapse
Affiliation(s)
- Edward Y Kim
- Department of Chemical and Biomolecular Engineering, The University of California, Berkeley, CA 94720, United States
| | | |
Collapse
|
18
|
Montelione GT. The Protein Structure Initiative: achievements and visions for the future. F1000 BIOLOGY REPORTS 2012; 4:7. [PMID: 22500193 PMCID: PMC3318194 DOI: 10.3410/b4-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Protein Structure Initiative (PSI) was established in 2000 by the National Institutes of General Medical Sciences with the long-term goal of providing 3D (three-dimensional) structural information for most proteins in nature. As advances in genomic sequencing, bioinformatics, homology modelling, and methods for rapid determination of 3D structures of proteins by X-ray crystallography and nuclear magnetic resonance (NMR) converged, it was proposed that our understanding of the biology of protein structure and evolution could be greatly enabled by ‘genomic-scale’ protein structure determination. Over the past 12 years, the PSI has evolved from a testing bed for new methods of sample and structure production to a core component of a wide range of biology programs.
Collapse
Affiliation(s)
- Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| |
Collapse
|
19
|
Shortridge MD, Triplet T, Revesz P, Griep MA, Powers R. Bacterial protein structures reveal phylum dependent divergence. Comput Biol Chem 2011; 35:24-33. [PMID: 21315656 DOI: 10.1016/j.compbiolchem.2010.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 12/28/2010] [Accepted: 12/29/2010] [Indexed: 01/26/2023]
Abstract
Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As expected, the analysis demonstrates a sharp structural divergence between the bacterial phyla Firmicutes and Proteobacteria. Additionally, each COG had a distinct sequence/structure relationship, indicating that different evolutionary pressures affect the degree of structural divergence. However, our analysis also shows the relative drift rate between sequence identity and structure divergence remains constant.
Collapse
Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Nebraska-Lincoln, 68588-0304, United States
| | | | | | | | | |
Collapse
|
20
|
Genetic analysis of the protein shell of the microcompartments involved in coenzyme B12-dependent 1,2-propanediol degradation by Salmonella. J Bacteriol 2011; 193:1385-92. [PMID: 21239588 DOI: 10.1128/jb.01473-10] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Hundreds of bacterial species use microcompartments (MCPs) to optimize metabolic pathways that have toxic or volatile intermediates. MCPs consist of a protein shell encapsulating specific metabolic enzymes. In Salmonella, an MCP is used for 1,2-propanediol utilization (Pdu MCP). The shell of this MCP is composed of eight different types of polypeptides, but their specific functions are uncertain. Here, we individually deleted the eight genes encoding the shell proteins of the Pdu MCP. The effects of each mutation on 1,2-PD degradation and MCP structure were determined by electron microscopy and growth studies. Deletion of the pduBB', pduJ, or pduN gene severely impaired MCP formation, and the observed defects were consistent with roles as facet, edge, or vertex protein, respectively. Metabolite measurements showed that pduA, pduBB', pduJ, or pduN deletion mutants accumulated propionaldehyde to toxic levels during 1,2-PD catabolism, indicating that the integrity of the shell was disrupted. Deletion of the pduK, pduT, or pduU gene did not substantially affect MCP structure or propionaldehyde accumulation, suggesting they are nonessential to MCP formation. However, the pduU or pduT deletion mutants grew more slowly than the wild type on 1,2-PD at saturating B(12), indicating that they are needed for maximal activity of the 1,2-PD degradative enzymes encased within the MCP shell. Considering recent crystallography studies, this suggests that PduT and PduU may mediate the transport of enzyme substrates/cofactors across the MCP shell. Interestingly, a pduK deletion caused MCP aggregation, suggesting a role in the spatial organization of MCP within the cytoplasm or perhaps in segregation at cell division.
Collapse
|
21
|
Abstract
Bacterial microcompartments (BMCs) are organelles composed entirely of protein. They promote specific metabolic processes by encapsulating and colocalizing enzymes with their substrates and cofactors, by protecting vulnerable enzymes in a defined microenvironment, and by sequestering toxic or volatile intermediates. Prototypes of the BMCs are the carboxysomes of autotrophic bacteria. However, structures of similar polyhedral shape are being discovered in an ever-increasing number of heterotrophic bacteria, where they participate in the utilization of specialty carbon and energy sources. Comparative genomics reveals that the potential for this type of compartmentalization is widespread across bacterial phyla and suggests that genetic modules encoding BMCs are frequently laterally transferred among bacteria. The diverse functions of these BMCs suggest that they contribute to metabolic innovation in bacteria in a broad range of environments.
Collapse
Affiliation(s)
- Cheryl A Kerfeld
- U.S. Department of Energy-Joint Genome Institute, Walnut Creek, California 94598, USA.
| | | | | |
Collapse
|
22
|
Triplet T, Shortridge MD, Griep MA, Stark JL, Powers R, Revesz P. PROFESS: a PROtein function, evolution, structure and sequence database. Database (Oxford) 2010; 2010:baq011. [PMID: 20624718 PMCID: PMC2911846 DOI: 10.1093/database/baq011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 06/03/2010] [Accepted: 06/06/2010] [Indexed: 11/13/2022]
Abstract
The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are approximately 1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein-protein interaction networks. Database URL: http://cse.unl.edu/~profess/
Collapse
Affiliation(s)
- Thomas Triplet
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Matthew D. Shortridge
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Mark A. Griep
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Jaime L. Stark
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Robert Powers
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Peter Revesz
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| |
Collapse
|
23
|
Ethanolamine utilization in bacterial pathogens: roles and regulation. Nat Rev Microbiol 2010; 8:290-5. [PMID: 20234377 DOI: 10.1038/nrmicro2334] [Citation(s) in RCA: 230] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ethanolamine is a compound that can be readily derived from cell membranes and that some bacteria can use as a source of carbon and/or nitrogen. The complex biology and chemistry of this process has been under investigation since the 1970s, primarily in one or two species. However, recent investigations into ethanolamine utilization have revealed important and intriguing differences in gene content and regulatory mechanisms among the bacteria that harbour this catabolic ability. In addition, many reports have connected this process to bacterial pathogenesis. In this Progress article, I discuss the latest research on the phylogeny and regulation of ethanolamine utilization and its possible roles in bacterial pathogenesis.
Collapse
|
24
|
Abstract
Some bacteria contain organelles or microcompartments consisting of a large virion-like protein shell encapsulating sequentially acting enzymes. These organized microcompartments serve to enhance or protect key metabolic pathways inside the cell. The variety of bacterial microcompartments provide diverse metabolic functions, ranging from CO(2) fixation to the degradation of small organic molecules. Yet they share an evolutionarily related shell, which is defined by a conserved protein domain that is widely distributed across the bacterial kingdom. Structural studies on a number of these bacterial microcompartment shell proteins are illuminating the architecture of the shell and highlighting its critical role in controlling molecular transport into and out of microcompartments. Current structural, evolutionary, and mechanistic ideas are discussed, along with genomic studies for exploring the function and diversity of this family of bacterial organelles.
Collapse
Affiliation(s)
- Todd O Yeates
- Department of Chemistry and Biochemistry, Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095, USA.
| | | | | |
Collapse
|
25
|
Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment. Proc Natl Acad Sci U S A 2009; 106:8883-7. [PMID: 19451619 DOI: 10.1073/pnas.0902324106] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial microcompartments (BMCs) are specialized organelles that use proteinaceous membranes to confine chemical reaction spaces. The ethanolamine ammonialyase microcompartment of Escherichia coli represents such a class of cytosolic organelles that enables bacteria to survive on small organic molecules such as ethanolamine as the sole source for carbon and nitrogen. We present here the crystal structure of the shell protein EutL at 2.2-A resolution. With 219 residues, it is the largest representative of this BMC's shell proteins. In the crystal, EutL forms a trimer that exhibits a hexagonally shaped tile structure. The tiles arrange into a tightly packed 2D array that is likely to resemble the proteinaceous membrane of the intact BMC. In contrast to other BMC shell proteins, which have only 1 pore per tile, EutL exhibits 3 pores per tile, thereby significantly increasing the overall porosity of this protein membrane. Each of the individual pores is lined with negatively charged residues and aromatic residues that are proposed to facilitate passive transport of specific solutes. The characteristic shape of the hexagonal tile, which is also found in the microcompartments of carbon-fixating bacteria, may present an inherent and fundamental building unit that may provide a general explanation for the formation of differently sized microcompartments.
Collapse
|
26
|
Beeby M, Bobik TA, Yeates TO. Exploiting genomic patterns to discover new supramolecular protein assemblies. Protein Sci 2009; 18:69-79. [PMID: 19177352 PMCID: PMC2708037 DOI: 10.1002/pro.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 09/19/2008] [Accepted: 09/22/2008] [Indexed: 01/29/2023]
Abstract
Bacterial microcompartments are supramolecular protein assemblies that function as bacterial organelles by compartmentalizing particular enzymes and metabolic intermediates. The outer shells of these microcompartments are assembled from multiple paralogous structural proteins. Because the paralogs are required to assemble together, their genes are often transcribed together from the same operon, giving rise to a distinctive genomic pattern: multiple, typically small, paralogous proteins encoded in close proximity on the bacterial chromosome. To investigate the generality of this pattern in supramolecular assemblies, we employed a comparative genomics approach to search for protein families that show the same kind of genomic pattern as that exhibited by bacterial microcompartments. The results indicate that a variety of large supramolecular assemblies fit the pattern, including bacterial gas vesicles, bacterial pili, and small heat-shock protein complexes. The search also retrieved several widely distributed protein families of presently unknown function. The proteins from one of these families were characterized experimentally and found to show a behavior indicative of supramolecular assembly. We conclude that cotranscribed paralogs are a common feature of diverse supramolecular assemblies, and a useful genomic signature for discovering new kinds of large protein assemblies from genomic data.
Collapse
Affiliation(s)
- Morgan Beeby
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los AngelesLos Angeles, California 90095
| | - Thomas A Bobik
- Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, Iowa 50011
| | - Todd O Yeates
- UCLA-DOE Institute for Genomics and Proteomics, University of California Los AngelesLos Angeles, California 90095
- Department of Chemistry and Biochemistry, University of California Los AngelesCalifornia 90095-1569
- Molecular Biology Institute, Paul D. Boyer HallLos Angeles, California 90095-1570
| |
Collapse
|
27
|
Parsons JB, Dinesh SD, Deery E, Leech HK, Brindley AA, Heldt D, Frank S, Smales CM, Lünsdorf H, Rambach A, Gass MH, Bleloch A, McClean KJ, Munro AW, Rigby SE, Warren MJ, Prentice MB. Biochemical and Structural Insights into Bacterial Organelle Form and Biogenesis. J Biol Chem 2008; 283:14366-75. [DOI: 10.1074/jbc.m709214200] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|
28
|
Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate. J Bacteriol 2008; 190:2966-71. [PMID: 18296526 DOI: 10.1128/jb.01925-07] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica grows on 1,2-propanediol (1,2-PD) in a coenzyme B(12)-dependent fashion. Prior studies showed that a bacterial microcompartment (MCP) is involved in this process and that an MCP-minus mutant undergoes a 20-h period of growth arrest during 1,2-PD degradation. It was previously proposed that growth arrest resulted from propionaldehyde toxicity, but no direct evidence was presented. Here, high-pressure liquid chromatography analyses of culture medium were used to show that the major products of aerobic 1,2-PD degradation are propionaldehyde, propionate, and 1-propanol. A MCP-minus mutant accumulated a level of propionaldehyde 10-fold higher than that of the wild type (1.6 mM compared to 15.7 mM), associating this compound with growth arrest. The addition of propionaldehyde to cultures of S. enterica caused growth arrest from 8 to 20 mM, but not at 4 mM, providing direct evidence for propionaldehyde toxicity. Studies also indicated that propionaldehyde was toxic due to the inhibition of respiratory processes, and the growth arrest ended when propionaldehyde was depleted primarily by conversion to propionate and 1-propanol and secondarily due to volatility. The Ames test was used to show that propionaldehyde is a mutagen and that mutation frequencies are increased in MCP-minus mutants during 1,2-PD degradation. We propose that a primary function of the MCPs involved in 1,2-PD degradation is the mitigation of toxicity and DNA damage by propionaldehyde.
Collapse
|