51
|
Evidence that the metabolite repair enzyme NAD(P)HX epimerase has a moonlighting function. Biosci Rep 2018; 38:BSR20180223. [PMID: 29654173 PMCID: PMC5938422 DOI: 10.1042/bsr20180223] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/04/2018] [Accepted: 04/09/2018] [Indexed: 11/25/2022] Open
Abstract
NAD(P)H-hydrate epimerase (EC 5.1.99.6) is known to help repair NAD(P)H hydrates (NAD(P)HX), which are damage products existing as R and S epimers. The S epimer is reconverted to NAD(P)H by a dehydratase; the epimerase facilitates epimer interconversion. Epimerase deficiency in humans causes a lethal disorder attributed to NADHX accumulation. However, bioinformatic evidence suggest caution about this attribution by predicting that the epimerase has a second function connected to vitamin B6 (pyridoxal 5′-phosphate and related compounds). Specifically, (i) the epimerase is fused to a B6 salvage enzyme in plants, (ii) epimerase genes cluster on the chromosome with B6-related genes in bacteria, and (iii) epimerase and B6-related genes are coexpressed in yeast and Arabidopsis. The predicted second function was explored in Escherichia coli, whose epimerase and dehydratase are fused and encoded by yjeF. The putative NAD(P)HX epimerase active site has a conserved lysine residue (K192 in E. coli YjeF). Changing this residue to alanine cut in vitro epimerase activity by ≥95% but did not affect dehydratase activity. Mutant cells carrying the K192A mutation had essentially normal NAD(P)HX dehydratase activity and NAD(P)HX levels, showing that the mutation had little impact on NAD(P)HX repair in vivo. However, these cells showed metabolome changes, particularly in amino acids, which exceeded those in cells lacking the entire yjeF gene. The K192A mutant cells also had reduced levels of ‘free’ (i.e. weakly bound or unbound) pyridoxal 5'-phosphate. These results provide circumstantial evidence that the epimerase has a metabolic function beyond NAD(P)HX repair and that this function involves vitamin B6.
Collapse
|
52
|
Kumar A, Karthikeyan S. Crystal structure of the MSMEG_4306 gene product from Mycobacterium smegmatis. Acta Crystallogr F Struct Biol Commun 2018; 74:166-173. [PMID: 29497021 PMCID: PMC5947703 DOI: 10.1107/s2053230x18002236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 02/06/2018] [Indexed: 12/31/2022] Open
Abstract
The MSMEG_4306 gene from Mycobacterium smegmatis encodes a protein of unknown function with 242 amino-acid residues that contains a conserved zinc-ribbon domain at its C-terminus. Here, the crystal structure of MSMEG_4306 determined by the single-wavelength anomalous dispersion method using just one zinc ion co-purified with the protein is reported. The crystal structure of MSMEG_4306 shows a coiled-coil helix domain in the N-terminal region and a zinc-ribbon domain in the C-terminal region. A structural similarity search against the Protein Data Bank using MSMEG_4306 as a query revealed two similar structures, namely CT398 from Chlamydia trachomatis and HP0958 from Helicobacter pylori, although they share only ∼15% sequence identity with MSMEG_4306. Based on comparative analysis, it is predicted that MSMEG_4306 may be involved in secretion systems, possibly by interacting with multiple proteins or nucleic acids.
Collapse
Affiliation(s)
- Adarsh Kumar
- CSIR – Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India
| | - Subramanian Karthikeyan
- CSIR – Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh 160 036, India
| |
Collapse
|
53
|
Pereira RVV, Carroll LM, Lima S, Foditsch C, Siler JD, Bicalho RC, Warnick LD. Impacts of feeding preweaned calves milk containing drug residues on the functional profile of the fecal microbiota. Sci Rep 2018; 8:554. [PMID: 29323259 PMCID: PMC5764986 DOI: 10.1038/s41598-017-19021-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022] Open
Abstract
Feeding drug residue-containing milk to calves is common worldwide and no information is currently available on the impact on the functional profile of the fecal microbiota. Our objective was to characterize the functional profile of the fecal microbiota of preweaned dairy calves fed raw milk with residual concentrations of antimicrobials commonly found in waste milk from birth to weaning. Calves were assigned to a controlled feeding trial being fed milk with no drug residues or milk with antibiotic residues. Fecal samples collected from each calf once a week starting at birth, prior to the first feeding in the trial, until 6 weeks of age. Antibiotic residues resulted in a significant difference in relative abundance of microbial cell functions, especially with genes linked with stress response, regulation and cell signaling, and nitrogen metabolism. These changes could directly impacts selection and dissemination of virulence and antimicrobial. Our data also identified a strong association between age in weeks and abundance of Resistance to Antibiotics and Toxic Compounds. Findings from this study support the hypothesis that drug residues, even at very low concentrations, impact the gut microbiota of calves and result in changes in the functional profile of microbial populations.
Collapse
Affiliation(s)
| | - Laura M Carroll
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Svetlana Lima
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Carla Foditsch
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Julie D Siler
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Rodrigo Carvalho Bicalho
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| | - Lorin D Warnick
- College of Veterinary Medicine, University of California Davis, Davis, CA, USA
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States of America
| |
Collapse
|
54
|
Lai Z, Tsugawa H, Wohlgemuth G, Mehta S, Mueller M, Zheng Y, Ogiwara A, Meissen J, Showalter M, Takeuchi K, Kind T, Beal P, Arita M, Fiehn O. Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nat Methods 2018; 15:53-56. [PMID: 29176591 PMCID: PMC6358022 DOI: 10.1038/nmeth.4512] [Citation(s) in RCA: 305] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/26/2017] [Indexed: 12/31/2022]
Abstract
Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives.
Collapse
Affiliation(s)
- Zijuan Lai
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
- Department of Chemistry, UC Davis, Davis, California USA
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa,
Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa,
Japan
| | - Gert Wohlgemuth
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Sajjan Mehta
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Matthew Mueller
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Yuxuan Zheng
- Department of Chemistry, UC Davis, Davis, California USA
| | | | - John Meissen
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Megan Showalter
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Kohei Takeuchi
- Perfume Development Research Laboratory, Kao Corporation, Sumida,
Tokyo, Japan
| | - Tobias Kind
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
| | - Peter Beal
- Department of Chemistry, UC Davis, Davis, California USA
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa,
Japan
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis, Davis, California
USA
- Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi
Arabia
| |
Collapse
|
55
|
Ellens KW, Christian N, Singh C, Satagopam VP, May P, Linster CL. Confronting the catalytic dark matter encoded by sequenced genomes. Nucleic Acids Res 2017; 45:11495-11514. [PMID: 29059321 PMCID: PMC5714238 DOI: 10.1093/nar/gkx937] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 10/03/2017] [Indexed: 01/02/2023] Open
Abstract
The post-genomic era has provided researchers with a deluge of protein sequences. However, a significant fraction of the proteins encoded by sequenced genomes remains without an identified function. Here, we aim at determining how many enzymes of uncertain or unknown function are still present in the Saccharomyces cerevisiae and human proteomes. Using information available in the Swiss-Prot, BRENDA and KEGG databases in combination with a Hidden Markov Model-based method, we estimate that >600 yeast and 2000 human proteins (>30% of their proteins of unknown function) are enzymes whose precise function(s) remain(s) to be determined. This illustrates the impressive scale of the ‘unknown enzyme problem’. We extensively review classical biochemical as well as more recent systematic experimental and computational approaches that can be used to support enzyme function discovery research. Finally, we discuss the possible roles of the elusive catalysts in light of recent developments in the fields of enzymology and metabolism as well as the significance of the unknown enzyme problem in the context of metabolic modeling, metabolic engineering and rare disease research.
Collapse
Affiliation(s)
- Kenneth W Ellens
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Nils Christian
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Charandeep Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Venkata P Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| |
Collapse
|
56
|
Sun J, Jeffryes JG, Henry CS, Bruner SD, Hanson AD. Metabolite damage and repair in metabolic engineering design. Metab Eng 2017; 44:150-159. [PMID: 29030275 DOI: 10.1016/j.ymben.2017.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/21/2017] [Accepted: 10/09/2017] [Indexed: 01/05/2023]
Abstract
The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields, and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects.
Collapse
Affiliation(s)
- Jiayi Sun
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - James G Jeffryes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA; Computation Institute, The University of Chicago, Chicago, IL, USA
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
57
|
Niehaus TD, Elbadawi-Sidhu M, de Crécy-Lagard V, Fiehn O, Hanson AD. Discovery of a widespread prokaryotic 5-oxoprolinase that was hiding in plain sight. J Biol Chem 2017; 292:16360-16367. [PMID: 28830929 DOI: 10.1074/jbc.m117.805028] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/18/2017] [Indexed: 11/06/2022] Open
Abstract
5-Oxoproline (OP) is well-known as an enzymatic intermediate in the eukaryotic γ-glutamyl cycle, but it is also an unavoidable damage product formed spontaneously from glutamine and other sources. Eukaryotes metabolize OP via an ATP-dependent 5-oxoprolinase; most prokaryotes lack homologs of this enzyme (and the γ-glutamyl cycle) but are predicted to have some way to dispose of OP if its spontaneous formation in vivo is significant. Comparative analysis of prokaryotic genomes showed that the gene encoding pyroglutamyl peptidase, which removes N-terminal OP residues, clusters in diverse genomes with genes specifying homologs of a fungal lactamase (renamed prokaryotic 5-oxoprolinase A, pxpA) and homologs of allophanate hydrolase subunits (renamed pxpB and pxpC). Inactivation of Bacillus subtilis pxpA, pxpB, or pxpC genes slowed growth, caused OP accumulation in cells and medium, and prevented use of OP as a nitrogen source. Assays of cell lysates showed that ATP-dependent 5-oxoprolinase activity disappeared when pxpA, pxpB, or pxpC was inactivated. 5-Oxoprolinase activity could be reconstituted in vitro by mixing recombinant B. subtilis PxpA, PxpB, and PxpC proteins. In addition, overexpressing Escherichia coli pxpABC genes in E. coli increased 5-oxoprolinase activity in lysates ≥1700-fold. This work shows that OP is a major universal metabolite damage product and that OP disposal systems are common in all domains of life. Furthermore, it illustrates how easily metabolite damage and damage-control systems can be overlooked, even for central metabolites in model organisms.
Collapse
Affiliation(s)
- Thomas D Niehaus
- From the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611,
| | - Mona Elbadawi-Sidhu
- the West Coast Metabolomics Center, University of California Davis, Davis, California 95616, and
| | - Valérie de Crécy-Lagard
- the Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611
| | - Oliver Fiehn
- the West Coast Metabolomics Center, University of California Davis, Davis, California 95616, and
| | - Andrew D Hanson
- From the Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611,
| |
Collapse
|
58
|
Schinn SM, Bradley W, Groesbeck A, Wu JC, Broadbent A, Bundy BC. Rapid in vitro screening for the location-dependent effects of unnatural amino acids on protein expression and activity. Biotechnol Bioeng 2017; 114:2412-2417. [PMID: 28398594 DOI: 10.1002/bit.26305] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 02/28/2017] [Accepted: 04/02/2017] [Indexed: 12/25/2022]
Abstract
The incorporation of unnatural amino acids (uAA) can introduce novel functional groups into proteins site-specifically, with important applications in basic sciences and protein engineering. However, uAA incorporation can impact protein expression and functional activity depending on its location within the protein-a process that is not yet completely understood and difficult to predict. Therefore, practical applications often necessitate a time-consuming optimization of uAA location by individual gene cloning, expressions, purification, and evaluations for each location tested. To address this limitation, we introduce a streamlined and versatile in vitro system to rapidly express and screen uAA-containing proteins without cumbersome cell culturing or purification procedures. We utilized this technology to simultaneously screen 24 different t4-lysozyme mutants with different uAA incorporation sites in a matter of hours, compared to weeks-long workflow of conventional methods. Screening data offered a mechanistic explanation to some effects of uAA incorporation on expression and activity. Despite these insights, rational prediction of such effects remained challenging, further confirming the value of a rapid screening approach. Biotechnol. Bioeng. 2017;114: 2412-2417. © 2017 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - William Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - Ashtyn Groesbeck
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - Jeffrey C Wu
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, Utah
| |
Collapse
|
59
|
Bastard K, Perret A, Mariage A, Bessonnet T, Pinet-Turpault A, Petit JL, Darii E, Bazire P, Vergne-Vaxelaire C, Brewee C, Debard A, Pellouin V, Besnard-Gonnet M, Artiguenave F, Médigue C, Vallenet D, Danchin A, Zaparucha A, Weissenbach J, Salanoubat M, de Berardinis V. Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nat Chem Biol 2017; 13:858-866. [PMID: 28581482 DOI: 10.1038/nchembio.2397] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
Experimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases.
Collapse
Affiliation(s)
- Karine Bastard
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Alain Perret
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Aline Mariage
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Thomas Bessonnet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Agnès Pinet-Turpault
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Jean-Louis Petit
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Ekaterina Darii
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Pascal Bazire
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Carine Vergne-Vaxelaire
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Clémence Brewee
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Adrien Debard
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Virginie Pellouin
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Marielle Besnard-Gonnet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | | | - Claudine Médigue
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - David Vallenet
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Antoine Danchin
- Institute of Cardiometabolism and Nutrition (ICAN), Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Anne Zaparucha
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Jean Weissenbach
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Marcel Salanoubat
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| | - Véronique de Berardinis
- CEA, DRF, Genoscope, Evry, France.,CNRS, UMR8030 Génomique Métabolique, Evry, France.,Université d'Evry Val d'Essonne, Evry, France.,Université Paris-Saclay, Evry, France
| |
Collapse
|
60
|
Piergiorge RM, de Miranda AB, Guimarães AC, Catanho M. Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy? Genome Biol Evol 2017; 9:1624-1636. [PMID: 28854631 PMCID: PMC5737724 DOI: 10.1093/gbe/evx119] [Citation(s) in RCA: 9] [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] [Accepted: 07/04/2017] [Indexed: 12/12/2022] Open
Abstract
Since enzymes catalyze almost all chemical reactions that occur in living organisms, it is crucial that genes encoding such activities are correctly identified and functionally characterized. Several studies suggest that the fraction of enzymatic activities in which multiple events of independent origin have taken place during evolution is substantial. However, this topic is still poorly explored, and a comprehensive investigation of the occurrence, distribution, and implications of these events has not been done so far. Fundamental questions, such as how analogous enzymes originate, why so many events of independent origin have apparently occurred during evolution, and what are the reasons for the coexistence in the same organism of distinct enzymatic forms catalyzing the same reaction, remain unanswered. Also, several isofunctional enzymes are still not recognized as nonhomologous, even with substantial evidence indicating different evolutionary histories. In this work, we begin to investigate the biological significance of the cooccurrence of nonhomologous isofunctional enzymes in human metabolism, characterizing functional analogous enzymes identified in metabolic pathways annotated in the human genome. Our hypothesis is that the coexistence of multiple enzymatic forms might not be interpreted as functional redundancy. Instead, these enzymatic forms may be implicated in distinct (and probably relevant) biological roles.
Collapse
Affiliation(s)
- Rafael Mina Piergiorge
- Laboratório de Genômica Funcional e Bioinformática, Fiocruz, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil
| | - Antonio Basílio de Miranda
- Laboratório de Biologia Computacional e Sistemas, Fiocruz, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil
| | - Ana Carolina Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Fiocruz, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genômica Funcional e Bioinformática, Fiocruz, Instituto Oswaldo Cruz, Manguinhos, Rio de Janeiro, Brazil
| |
Collapse
|
61
|
Zallot R, Ross R, Chen WH, Bruner SD, Limbach PA, de Crécy-Lagard V. Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics. ACS Chem Biol 2017; 12:844-851. [PMID: 28128549 PMCID: PMC5495094 DOI: 10.1021/acschembio.6b01100] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The reduction of epoxyqueuosine (oQ)
is the last step in the synthesis
of the tRNA modification queuosine (Q). While the epoxyqueuosine reductase
(EC 1.17.99.6) enzymatic activity was first described 30 years ago,
the encoding gene queG was only identified in Escherichia coli in 2011. Interestingly, queG is absent from a large number of sequenced genomes that harbor Q
synthesis or salvage genes, suggesting the existence of an alternative
epoxyqueuosine reductase in these organisms. By analyzing phylogenetic
distributions, physical gene clustering, and fusions, members of the
Domain of Unknown Function 208 (DUF208) family were predicted to encode
for an alternative epoxyqueuosine reductase. This prediction was validated
with genetic methods. The Q modification is present in Lactobacillus
salivarius, an organism missing queG but
harboring the duf208 gene. Acinetobacter
baylyi ADP1 is one of the few organisms that harbor both
QueG and DUF208, and deletion of both corresponding genes was required
to observe the absence of Q and the accumulation of oQ in tRNA. Finally,
the conversion oQ to Q was restored in an E. coli queG mutant by complementation with plasmids harboring duf208 genes from different bacteria. Members of the DUF208 family are
not homologous to QueG enzymes, and thus, duf208 is
a non-orthologous replacement of queG. We propose
to name DUF208 encoding genes as queH. While QueH
contains conserved cysteines that could be involved in the coordination
of a Fe/S center in a similar fashion to what has been identified
in QueG, no cobalamin was identified associated with recombinant QueH
protein.
Collapse
Affiliation(s)
- Rémi Zallot
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| | - Robert Ross
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Wei-Hung Chen
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Patrick A. Limbach
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| |
Collapse
|
62
|
Fuhrer T, Zampieri M, Sévin DC, Sauer U, Zamboni N. Genomewide landscape of gene-metabolome associations in Escherichia coli. Mol Syst Biol 2017; 13:907. [PMID: 28093455 PMCID: PMC5293155 DOI: 10.15252/msb.20167150] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Metabolism is one of the best-understood cellular processes whose network topology of enzymatic reactions is determined by an organism's genome. The influence of genes on metabolite levels, however, remains largely unknown, particularly for the many genes encoding non-enzymatic proteins. Serendipitously, genomewide association studies explore the relationship between genetic variants and metabolite levels, but a comprehensive interaction network has remained elusive even for the simplest single-celled organisms. Here, we systematically mapped the association between > 3,800 single-gene deletions in the bacterium Escherichia coli and relative concentrations of > 7,000 intracellular metabolite ions. Beyond expected metabolic changes in the proximity to abolished enzyme activities, the association map reveals a largely unknown landscape of gene-metabolite interactions that are not represented in metabolic models. Therefore, the map provides a unique resource for assessing the genetic basis of metabolic changes and conversely hypothesizing metabolic consequences of genetic alterations. We illustrate this by predicting metabolism-related functions of 72 so far not annotated genes and by identifying key genes mediating the cellular response to environmental perturbations.
Collapse
Affiliation(s)
- Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| |
Collapse
|
63
|
Sévin DC, Fuhrer T, Zamboni N, Sauer U. Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat Methods 2016; 14:187-194. [DOI: 10.1038/nmeth.4103] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/19/2016] [Indexed: 12/14/2022]
|
64
|
Singh C, Glaab E, Linster CL. Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. J Biol Chem 2016; 292:1005-1028. [PMID: 27909055 DOI: 10.1074/jbc.m116.760744] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
Proteomes of even well characterized organisms still contain a high percentage of proteins with unknown or uncertain molecular and/or biological function. A significant fraction of those proteins is predicted to have catalytic properties. Here we aimed at identifying the function of the Saccharomyces cerevisiae Ydr109c protein and its human homolog FGGY, both of which belong to the broadly conserved FGGY family of carbohydrate kinases. Functionally identified members of this family phosphorylate 3- to 7-carbon sugars or sugar derivatives, but the endogenous substrate of S. cerevisiae Ydr109c and human FGGY has remained unknown. Untargeted metabolomics analysis of an S. cerevisiae deletion mutant of YDR109C revealed ribulose as one of the metabolites with the most significantly changed intracellular concentration as compared with a wild-type strain. In human HEK293 cells, ribulose could only be detected when ribitol was added to the cultivation medium, and under this condition, FGGY silencing led to ribulose accumulation. Biochemical characterization of the recombinant purified Ydr109c and FGGY proteins showed a clear substrate preference of both kinases for d-ribulose over a range of other sugars and sugar derivatives tested, including l-ribulose. Detailed sequence and structural analyses of Ydr109c and FGGY as well as homologs thereof furthermore allowed the definition of a 5-residue d-ribulokinase signature motif (TCSLV). The physiological role of the herein identified eukaryotic d-ribulokinase remains unclear, but we speculate that S. cerevisiae Ydr109c and human FGGY could act as metabolite repair enzymes, serving to re-phosphorylate free d-ribulose generated by promiscuous phosphatases from d-ribulose 5-phosphate. In human cells, FGGY can additionally participate in ribitol metabolism.
Collapse
Affiliation(s)
- Charandeep Singh
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| |
Collapse
|
65
|
Mimura M, Zallot R, Niehaus TD, Hasnain G, Gidda SK, Nguyen TND, Anderson EM, Mullen RT, Brown G, Yakunin AF, de Crécy-Lagard V, Gregory JF, McCarty DR, Hanson AD. Arabidopsis TH2 Encodes the Orphan Enzyme Thiamin Monophosphate Phosphatase. THE PLANT CELL 2016; 28:2683-2696. [PMID: 27677881 PMCID: PMC5134987 DOI: 10.1105/tpc.16.00600] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 05/18/2023]
Abstract
To synthesize the cofactor thiamin diphosphate (ThDP), plants must first hydrolyze thiamin monophosphate (ThMP) to thiamin, but dedicated enzymes for this hydrolysis step were unknown and widely doubted to exist. The classical thiamin-requiring th2-1 mutation in Arabidopsis thaliana was shown to reduce ThDP levels by half and to increase ThMP levels 5-fold, implying that the THIAMIN REQUIRING2 (TH2) gene product could be a dedicated ThMP phosphatase. Genomic and transcriptomic data indicated that TH2 corresponds to At5g32470, encoding a HAD (haloacid dehalogenase) family phosphatase fused to a TenA (thiamin salvage) family protein. Like the th2-1 mutant, an insertional mutant of At5g32470 accumulated ThMP, and the thiamin requirement of the th2-1 mutant was complemented by wild-type At5g32470 Complementation tests in Escherichia coli and enzyme assays with recombinant proteins confirmed that At5g32470 and its maize (Zea mays) orthologs GRMZM2G148896 and GRMZM2G078283 are ThMP-selective phosphatases whose activity resides in the HAD domain and that the At5g32470 TenA domain has the expected thiamin salvage activity. In vitro and in vivo experiments showed that alternative translation start sites direct the At5g32470 protein to the cytosol and potentially also to mitochondria. Our findings establish that plants have a dedicated ThMP phosphatase and indicate that modest (50%) ThDP depletion can produce severe deficiency symptoms.
Collapse
Affiliation(s)
- Manaki Mimura
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Thuy N D Nguyen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Erin M Anderson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | | | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, Florida 32611
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| |
Collapse
|
66
|
Zallot R, Harrison KJ, Kolaczkowski B, de Crécy-Lagard V. Functional Annotations of Paralogs: A Blessing and a Curse. Life (Basel) 2016; 6:life6030039. [PMID: 27618105 PMCID: PMC5041015 DOI: 10.3390/life6030039] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 12/15/2022] Open
Abstract
Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines. Here we describe how integrating evolutionary and functional information such as genome context, phylogeny, metabolic reconstruction and signature motifs may be required to correctly annotate multifunctional families. These integrative analyses can also lead to the discovery of novel gene functions, as hints from specific subgroups can guide the functional characterization of other members of the family. We demonstrate how careful manual curation processes using comparative genomics can disambiguate subgroups within large multifunctional families and discover their functions. We present the COG0720 protein family as a case study. We also discuss strategies to automate this process to improve the accuracy of genome functional annotation pipelines.
Collapse
Affiliation(s)
- Rémi Zallot
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Katherine J Harrison
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Bryan Kolaczkowski
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
67
|
Nguyen NN, Srihari S, Leong HW, Chong KF. EnzDP: improved enzyme annotation for metabolic network reconstruction based on domain composition profiles. J Bioinform Comput Biol 2016; 13:1543003. [PMID: 26542446 DOI: 10.1142/s0219720015430039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Determining the entire complement of enzymes and their enzymatic functions is a fundamental step for reconstructing the metabolic network of cells. High quality enzyme annotation helps in enhancing metabolic networks reconstructed from the genome, especially by reducing gaps and increasing the enzyme coverage. Currently, structure-based and network-based approaches can only cover a limited number of enzyme families, and the accuracy of homology-based approaches can be further improved. Bottom-up homology-based approach improves the coverage by rebuilding Hidden Markov Model (HMM) profiles for all known enzymes. However, its clustering procedure relies firmly on BLAST similarity score, ignoring protein domains/patterns, and is sensitive to changes in cut-off thresholds. Here, we use functional domain architecture to score the association between domain families and enzyme families (Domain-Enzyme Association Scoring, DEAS). The DEAS score is used to calculate the similarity between proteins, which is then used in clustering procedure, instead of using sequence similarity score. We improve the enzyme annotation protocol using a stringent classification procedure, and by choosing optimal threshold settings and checking for active sites. Our analysis shows that our stringent protocol EnzDP can cover up to 90% of enzyme families available in Swiss-Prot. It achieves a high accuracy of 94.5% based on five-fold cross-validation. EnzDP outperforms existing methods across several testing scenarios. Thus, EnzDP serves as a reliable automated tool for enzyme annotation and metabolic network reconstruction. Available at: www.comp.nus.edu.sg/~nguyennn/EnzDP .
Collapse
Affiliation(s)
- Nam-Ninh Nguyen
- Department of Computer Science, National University of Singapore, Singapore 117417, Singapore
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland 4067, Australia
| | - Hon Wai Leong
- Department of Computer Science, National University of Singapore, Singapore 117417, Singapore
| | - Ket-Fah Chong
- Department of Computer Science, National University of Singapore, Singapore 117417, Singapore
| |
Collapse
|
68
|
Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, de Crécy-Lagard V. Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite. ACS Chem Biol 2016; 11:2304-11. [PMID: 27294475 DOI: 10.1021/acschembio.6b00279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DUF1537 is a novel family of kinases identified by comparative genomic approaches. The family is widespread and found in all sequenced plant genomes and 16% of sequenced bacterial genomes. DUF1537 is not a monofunctional family and contains subgroups that can be separated by phylogenetic and genome neighborhood context analyses. A subset of the DUF1537 proteins is strongly associated by physical clustering and gene fusion with the PdxA2 family, demonstrated here to be a functional paralog of the 4-phosphohydroxy-l-threonine dehydrogenase enzyme (PdxA), a central enzyme in the synthesis of pyridoxal-5'-phosphate (PLP) in proteobacteria. Some members of this DUF1537 subgroup phosphorylate l-4-hydroxythreonine (4HT) into 4-phosphohydroxy-l-threonine (4PHT), the substrate of PdxA, in vitro and in vivo. This provides an alternative route to PLP from the toxic antimetabolite 4HT that can be directly generated from the toxic intermediate glycolaldehyde. Although the kinetic and physical clustering data indicate that these functions in PLP synthesis are not the main roles of the DUF1537-PdxA2 enzymes, genetic and physiological data suggest these side activities function has been maintained in diverse sets of organisms.
Collapse
Affiliation(s)
- Jennifer J. Thiaville
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Jake Flood
- Department
of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado United States
| | - Svetlana Yurgel
- Dalhousie University, 6299 South
St., Halifax, NS B3H 4R2, Canada
| | - Laurence Prunetti
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | | | - Geoffrey Hutinet
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Farhad Forouhar
- Department
of Biological Sciences, Columbia University, New York, New York, United States
| | - Xinshuai Zhang
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Venkateswaran Ganesan
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Patrick Reddy
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center, UC Davis, Davis, California, United States
- King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia
| | - J. A. Gerlt
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John F. Hunt
- Department
of Biological Sciences, Columbia University, New York, New York, United States
| | - Shelley D. Copley
- Department
of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| |
Collapse
|
69
|
Van Dyke MW, Beyer MD, Clay E, Hiam KJ, McMurry JL, Xie Y. Identification of Preferred DNA-Binding Sites for the Thermus thermophilus Transcriptional Regulator SbtR by the Combinatorial Approach REPSA. PLoS One 2016; 11:e0159408. [PMID: 27428627 PMCID: PMC4948773 DOI: 10.1371/journal.pone.0159408] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/02/2016] [Indexed: 01/04/2023] Open
Abstract
One of the first steps towards elucidating the biological function of a putative transcriptional regulator is to ascertain its preferred DNA-binding sequences. This may be rapidly and effectively achieved through the application of a combinatorial approach, one involving very large numbers of randomized oligonucleotides and reiterative selection and amplification steps to enrich for high-affinity nucleic acid-binding sequences. Previously, we had developed the novel combinatorial approach Restriction Endonuclease Protection, Selection and Amplification (REPSA), which relies not on the physical separation of ligand-nucleic acid complexes but instead selects on the basis of ligand-dependent inhibition of enzymatic template inactivation, specifically cleavage by type IIS restriction endonucleases. Thus, no prior knowledge of the ligand is required for REPSA, making it more amenable for discovery purposes. Here we describe using REPSA, massively parallel sequencing, and bioinformatics to identify the preferred DNA-binding sites for the transcriptional regulator SbtR, encoded by the TTHA0167 gene from the model extreme thermophile Thermus thermophilus HB8. From the resulting position weight matrix, we can identify multiple operons potentially regulated by SbtR and postulate a biological role for this protein in regulating extracellular transport processes. Our study provides a proof-of-concept for the application of REPSA for the identification of preferred DNA-binding sites for orphan transcriptional regulators and a first step towards determining their possible biological roles.
Collapse
Affiliation(s)
- Michael W. Van Dyke
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
- * E-mail:
| | - Matthew D. Beyer
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Emily Clay
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Kamir J. Hiam
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Jonathan L. McMurry
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Ying Xie
- Department of Computer Science, Kennesaw State University, Kennesaw, Georgia, United States of America
| |
Collapse
|
70
|
A family of metal-dependent phosphatases implicated in metabolite damage-control. Nat Chem Biol 2016; 12:621-7. [PMID: 27322068 DOI: 10.1038/nchembio.2108] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 03/30/2016] [Indexed: 12/31/2022]
Abstract
DUF89 family proteins occur widely in both prokaryotes and eukaryotes, but their functions are unknown. Here we define three DUF89 subfamilies (I, II, and III), with subfamily II being split into stand-alone proteins and proteins fused to pantothenate kinase (PanK). We demonstrated that DUF89 proteins have metal-dependent phosphatase activity against reactive phosphoesters or their damaged forms, notably sugar phosphates (subfamilies II and III), phosphopantetheine and its S-sulfonate or sulfonate (subfamily II-PanK fusions), and nucleotides (subfamily I). Genetic and comparative genomic data strongly associated DUF89 genes with phosphoester metabolism. The crystal structure of the yeast (Saccharomyces cerevisiae) subfamily III protein YMR027W revealed a novel phosphatase active site with fructose 6-phosphate and Mg(2+) bound near conserved signature residues Asp254 and Asn255 that are critical for activity. These findings indicate that DUF89 proteins are previously unrecognized hydrolases whose characteristic in vivo function is to limit potentially harmful buildups of normal or damaged phosphometabolites.
Collapse
|
71
|
A scalable strategy for high-throughput GFP tagging of endogenous human proteins. Proc Natl Acad Sci U S A 2016; 113:E3501-8. [PMID: 27274053 DOI: 10.1073/pnas.1606731113] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A central challenge of the postgenomic era is to comprehensively characterize the cellular role of the ∼20,000 proteins encoded in the human genome. To systematically study protein function in a native cellular background, libraries of human cell lines expressing proteins tagged with a functional sequence at their endogenous loci would be very valuable. Here, using electroporation of Cas9 nuclease/single-guide RNA ribonucleoproteins and taking advantage of a split-GFP system, we describe a scalable method for the robust, scarless, and specific tagging of endogenous human genes with GFP. Our approach requires no molecular cloning and allows a large number of cell lines to be processed in parallel. We demonstrate the scalability of our method by targeting 48 human genes and show that the resulting GFP fluorescence correlates with protein expression levels. We next present how our protocols can be easily adapted for the tagging of a given target with GFP repeats, critically enabling the study of low-abundance proteins. Finally, we show that our GFP tagging approach allows the biochemical isolation of native protein complexes for proteomic studies. Taken together, our results pave the way for the large-scale generation of endogenously tagged human cell lines for the proteome-wide analysis of protein localization and interaction networks in a native cellular context.
Collapse
|
72
|
Hanson AD, Henry CS, Fiehn O, de Crécy-Lagard V. Metabolite Damage and Metabolite Damage Control in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:131-52. [PMID: 26667673 DOI: 10.1146/annurev-arplant-043015-111648] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
It is increasingly clear that (a) many metabolites undergo spontaneous or enzyme-catalyzed side reactions in vivo, (b) the damaged metabolites formed by these reactions can be harmful, and (c) organisms have biochemical systems that limit the buildup of damaged metabolites. These damage-control systems either return a damaged molecule to its pristine state (metabolite repair) or convert harmful molecules to harmless ones (damage preemption). Because all organisms share a core set of metabolites that suffer the same chemical and enzymatic damage reactions, certain damage-control systems are widely conserved across the kingdoms of life. Relatively few damage reactions and damage-control systems are well known. Uncovering new damage reactions and identifying the corresponding damaged metabolites, damage-control genes, and enzymes demands a coordinated mix of chemistry, metabolomics, cheminformatics, biochemistry, and comparative genomics. This review illustrates the above points using examples from plants, which are at least as prone to metabolite damage as other organisms.
Collapse
Affiliation(s)
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois 60439;
- Computation Institute, University of Chicago, Chicago, Illinois 60637
| | - Oliver Fiehn
- Genome Center, University of California, Davis, California 95616;
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida 32611; ,
| |
Collapse
|
73
|
Vianello A, Passamonti S. Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology. Biol Direct 2016; 11:7. [PMID: 26861860 PMCID: PMC4748562 DOI: 10.1186/s13062-016-0109-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022] Open
Abstract
Functional biologists, like Claude Bernard, ask "How?", meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Charles Darwin, asks "Why?", meaning that they search the causes of adaptation, survival and evolution (remote causes). Are these divergent views on what is life? The epistemological role of functional biology (molecular biology, but also biochemistry, physiology, cell biology and so forth) appears essential, for its capacity to identify several mechanisms of natural selection of new characters, individuals and populations. Nevertheless, several issues remain unsolved, such as orphan metabolic activities, i.e., adaptive functions still missing the identification of the underlying genes and proteins, and orphan genes, i.e., genes that bear no signature of evolutionary history, yet provide an organism with improved adaptation to environmental changes. In the framework of the Extended Synthesis, we suggest that the adaptive roles of any known function/structure are reappraised in terms of their capacity to warrant constancy of the internal environment (homeostasis), a concept that encompasses both proximal and remote causes.
Collapse
Affiliation(s)
- Angelo Vianello
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Udine, 33100, Udine, Italy.
| | - Sabina Passamonti
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, 34100, Trieste, Italy.
| |
Collapse
|
74
|
Bacterial and plant HAD enzymes catalyse a missing phosphatase step in thiamin diphosphate biosynthesis. Biochem J 2016; 473:157-66. [DOI: 10.1042/bj20150805] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/03/2015] [Indexed: 01/17/2023]
Abstract
To make thiamin diphosphate (ThDP), plants and many micro-organisms first dephosphorylate thiamin monophosphate (ThMP). This dephosphorylation has been thought to be mediated by non-specific enzymes. However, comparative genomic, genetic and biochemical evidences implicate specific HAD family phosphatases in bacteria and plants.
Collapse
|
75
|
Shi H, Schwender J. Mathematical models of plant metabolism. Curr Opin Biotechnol 2015; 37:143-152. [PMID: 26723012 DOI: 10.1016/j.copbio.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 11/24/2022]
Abstract
Among various modeling approaches in plant metabolic research, applications of Constraint-Based modeling are fast increasing in recent years, apparently driven by current advances in genomics and genome sequencing. Constraint-Based modeling, the functional analysis of metabolic networks at the whole cell or genome scale, is more difficult to apply to plants than to microbes. Here we discuss recent developments in Constraint-Based modeling in plants with focus on issues of model reconstruction and flux prediction. Another topic is the emerging application of integration of Constraint-Based modeling with omics data to increase predictive power. Furthermore, advances in experimental measurements of cellular fluxes by (13)C-Metabolic Flux Analysis are highlighted, including instationary (13)C-MFA used to probe autotrophic metabolism in photosynthetic tissue in the light.
Collapse
Affiliation(s)
- Hai Shi
- Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Jörg Schwender
- Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States.
| |
Collapse
|
76
|
Ponce-de-Leon M, Calle-Espinosa J, Peretó J, Montero F. Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PLoS One 2015; 10:e0143626. [PMID: 26629901 PMCID: PMC4668087 DOI: 10.1371/journal.pone.0143626] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/06/2015] [Indexed: 01/10/2023] Open
Abstract
Genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. With the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. The results showed that a large number of reactions (~22%) are blocked in all the models where they are present. To unravel the nature of such inconsistencies a metamodel was construed by joining the 130 models in a single network. This metamodel was manually curated using the unconnected modules approach, and then, it was used as a reference network to perform a gap-filling on each individual genome-scale model. Finally, a set of 36 models that had not been considered during the construction of the metamodel was used, as a proof of concept, to extend the metamodel with new biochemical information, and to assess its impact on gap-filling results. The analysis performed on the metamodel allowed to conclude: 1) the recurrent inconsistencies found in the models were already present in the metabolic database used during the reconstructions process; 2) the presence of inconsistencies in a metabolic database can be propagated to the reconstructed models; 3) there are reactions not manifested as blocked which are active as a consequence of some classes of artifacts, and; 4) the results of an automatic gap-filling are highly dependent on the consistency and completeness of the metamodel or metabolic database used as the reference network. In conclusion the consistency analysis should be applied to metabolic databases in order to detect and fill gaps as well as to detect and remove artifacts and redundant information.
Collapse
Affiliation(s)
- Miguel Ponce-de-Leon
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain
- * E-mail:
| | - Jorge Calle-Espinosa
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain
| | - Juli Peretó
- Departament de Bioquímica i Biologia Molecular and Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, C/José Beltrán 2, Paterna 46980, Spain
| | - Francisco Montero
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Ciudad Universitaria, Madrid 28045, Spain
| |
Collapse
|
77
|
Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE. De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 2015; 16:997. [PMID: 26602763 PMCID: PMC4658800 DOI: 10.1186/s12864-015-2225-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/17/2015] [Indexed: 01/13/2023] Open
Abstract
Background Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. Results In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. Conclusions This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2225-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Juan C Castro
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú. .,Círculo de Investigación en Plantas con Efecto en Salud (FONDECYT N° 010-2014), Lima, Perú.
| | - J Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum of Natural History, Chicago, IL, USA.
| | - Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Av. Abelardo Quiñones km 2.5, San Juan Bautista, Iquitos, Perú.
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | | | - Sixto A Imán
- Área de Conservación de Recursos Fitogenéticos, Instituto Nacional de Innovación Agraria (INIA), Calle San Roque 209, Iquitos, Perú.
| | - Luis A Cerdeira
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| | - Andersson E Medina
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| |
Collapse
|
78
|
Allen DK. Quantifying plant phenotypes with isotopic labeling & metabolic flux analysis. Curr Opin Biotechnol 2015; 37:45-52. [PMID: 26613198 DOI: 10.1016/j.copbio.2015.10.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/04/2015] [Accepted: 10/06/2015] [Indexed: 12/14/2022]
Abstract
Analyses of metabolic flux using stable isotopes in plants have traditionally been restricted to tissues with presumed homogeneous cell populations and long metabolic steady states such as developing seeds, cell suspensions, or cultured roots and root tips. It is now possible to describe these and other metabolically more dynamic tissues such as leaves in greater detail using novel methods in mass spectrometry, isotope labeling strategies, and transient labeling-based flux analyses. Such studies are necessary for a systems level description of plant function that more closely represents biological reality, and provides insights into the genes that will need to be modified as natural resources become ever more limited and environments change.
Collapse
Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| |
Collapse
|
79
|
Tomono T, Kojima H, Fukuchi S, Tohsato Y, Ito M. Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling. Biophys Physicobiol 2015; 12:57-68. [PMID: 27493855 PMCID: PMC4736839 DOI: 10.2142/biophysico.12.0_57] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/12/2015] [Indexed: 02/06/2023] Open
Abstract
Glycans play important roles in such cell-cell interactions as signaling and adhesion, including processes involved in pathogenic infections, cancers, and neurological diseases. Glycans are biosynthesized by multiple glycosyltransferases (GTs), which function sequentially. Excluding mucin-type O-glycosylation, the non-reducing terminus of glycans is biosynthesized in the Golgi apparatus after the reducing terminus is biosynthesized in the ER. In the present study, we performed genome-wide analyses of human GTs by investigating the degree of conservation of homologues in other organisms, as well as by elucidating the phylogenetic relationship between cephalochordates and urochordates, which has long been controversial in deuterostome phylogeny. We analyzed 173 human GTs and functionally linked glycan synthesis enzymes by phylogenetic profiling and clustering, compiled orthologous genes from the genomes of other organisms, and converted them into a binary sequence based on the presence (1) or absence (0) of orthologous genes in the genomes. Our results suggest that the non-reducing terminus of glycans is biosynthesized by newly evolved GTs. According to our analysis, the phylogenetic profiles of GTs resemble the phylogenetic tree of life, where deuterostomes, metazoans, and eukaryotes are resolved into separate branches. Lineage-specific GTs appear to play essential roles in the divergence of these particular lineages. We suggest that urochordates lose several genes that are conserved among metazoans, such as those expressing sialyltransferases, and that the Golgi apparatus acquires the ability to synthesize glycans after the ER acquires this function.
Collapse
Affiliation(s)
- Takayoshi Tomono
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Hisao Kojima
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Satoshi Fukuchi
- Department of Life Science and Informatics, Faculty of Engineering, Maebashi Institute of Technology, Gunma 371-0816, Japan
| | - Yukako Tohsato
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| |
Collapse
|
80
|
Niehaus TD, Thamm AMK, de Crécy-Lagard V, Hanson AD. Proteins of Unknown Biochemical Function: A Persistent Problem and a Roadmap to Help Overcome It. PLANT PHYSIOLOGY 2015; 169:1436-42. [PMID: 26269542 PMCID: PMC4634069 DOI: 10.1104/pp.15.00959] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/11/2015] [Indexed: 05/03/2023]
Abstract
The number of sequenced genomes is rapidly increasing, but functional annotation of the genes in these genomes lags far behind. Even in Arabidopsis (Arabidopsis thaliana), only approximately 40% of enzyme- and transporter-encoding genes have credible functional annotations, and this number is even lower in nonmodel plants. Functional characterization of unknown genes is a challenge, but various databases (e.g. for protein localization and coexpression) can be mined to provide clues. If homologous microbial genes exist-and about one-half the genes encoding unknown enzymes and transporters in Arabidopsis have microbial homologs-cross-kingdom comparative genomics can powerfully complement plant-based data. Multiple lines of evidence can strengthen predictions and warrant experimental characterization. In some cases, relatively quick tests in genetically tractable microbes can determine whether a prediction merits biochemical validation, which is costly and demands specialized skills.
Collapse
Affiliation(s)
- Thomas D Niehaus
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
| | - Antje M K Thamm
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
| | - Valérie de Crécy-Lagard
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
| | - Andrew D Hanson
- Horticultural Sciences Department (T.D.N., A.M.K.T., A.D.H.) and Microbiology and Cell Science Department (V.d.C.-L.), University of Florida, Gainesville, Florida 32611
| |
Collapse
|
81
|
Van Schaftingen E, Veiga-da-Cunha M, Linster CL. Enzyme complexity in intermediary metabolism. J Inherit Metab Dis 2015; 38:721-7. [PMID: 25700988 DOI: 10.1007/s10545-015-9821-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 01/30/2015] [Accepted: 02/03/2015] [Indexed: 10/24/2022]
Abstract
A good appraisal of the function of enzymes is essential for the understanding of inborn errors of metabolism. However, it is clear now that the 'one gene, one enzyme, one catalytic function' rule oversimplifies the actual situation. Genes often encode several related proteins, which may differ in their subcellular localisation, regulation or function. Furthermore, enzymes often show several catalytic activities. In some cases, this is because they are multifunctional, possessing two or more different active sites that catalyse different, physiologically related reactions. In enzymes with broad specificity or in multispecificity enzymes, a single type of catalytic site performs the same reaction on different physiological substrates at similar rates. Enzymes that act physiologically in only one reaction often show nonetheless substrate promiscuity: they act at low rates on compounds that resemble their physiological substrate(s), thus forming non-classical metabolites, which are in some cases eliminated by metabolite repair. In addition to their catalytic role, enzymes may have moonlighting functions, i.e. non-catalytic functions that are most often not related with their catalytic activity. Deficiency in such functions may participate in the phenotype of inborn errors of metabolism. Evolution has also made that some enzymes have lost their catalytic activity to become allosteric proteins.
Collapse
Affiliation(s)
- Emile Van Schaftingen
- Welbio and de Duve Institute, Université catholique de Louvain, Avenue Hippocrate 75, 1200, Brussels, Belgium,
| | | | | |
Collapse
|
82
|
Kuznetsova E, Nocek B, Brown G, Makarova KS, Flick R, Wolf YI, Khusnutdinova A, Evdokimova E, Jin K, Tan K, Hanson AD, Hasnain G, Zallot R, de Crécy-Lagard V, Babu M, Savchenko A, Joachimiak A, Edwards AM, Koonin EV, Yakunin AF. Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae: BIOCHEMICAL, STRUCTURAL, AND EVOLUTIONARY INSIGHTS. J Biol Chem 2015; 290:18678-98. [PMID: 26071590 DOI: 10.1074/jbc.m115.657916] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 12/15/2022] Open
Abstract
The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members.
Collapse
Affiliation(s)
- Ekaterina Kuznetsova
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Boguslaw Nocek
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Greg Brown
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Kira S Makarova
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Robert Flick
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Yuri I Wolf
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Anna Khusnutdinova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elena Evdokimova
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Ke Jin
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Kemin Tan
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Andrew D Hanson
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Ghulam Hasnain
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Rémi Zallot
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Valérie de Crécy-Lagard
- the Horticultural Sciences Department, Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Mohan Babu
- the Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada, and
| | - Alexei Savchenko
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Andrzej Joachimiak
- the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Aled M Edwards
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439
| | - Eugene V Koonin
- the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Alexander F Yakunin
- the Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada,
| |
Collapse
|
83
|
Niehaus TD, Gerdes S, Hodge-Hanson K, Zhukov A, Cooper AJL, ElBadawi-Sidhu M, Fiehn O, Downs DM, Hanson AD. Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family. BMC Genomics 2015; 16:382. [PMID: 25975565 PMCID: PMC4433059 DOI: 10.1186/s12864-015-1584-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/27/2015] [Indexed: 12/03/2022] Open
Abstract
Background It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5'-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions. Results Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5'-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate. Conclusions Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5'-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1584-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
| | - Svetlana Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.
| | | | - Aleksey Zhukov
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA.
| | - Arthur J L Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, 10595, USA.
| | - Mona ElBadawi-Sidhu
- Metabolomics Core, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.
| | - Oliver Fiehn
- Metabolomics Core, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA.
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
| |
Collapse
|
84
|
Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND. Data-driven integration of genome-scale regulatory and metabolic network models. Front Microbiol 2015; 6:409. [PMID: 25999934 PMCID: PMC4419725 DOI: 10.3389/fmicb.2015.00409] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/20/2015] [Indexed: 12/21/2022] Open
Abstract
Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert-a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.
Collapse
Affiliation(s)
- Saheed Imam
- Institute for Systems Biology Seattle, WA, USA
| | - Sascha Schäuble
- Institute for Systems Biology Seattle, WA, USA ; Jena University Language and Information Engineering Lab, Friedrich-Schiller-University Jena Jena, Germany
| | | | - Nitin S Baliga
- Institute for Systems Biology Seattle, WA, USA ; Departments of Biology and Microbiology, University of Washington Seattle, WA, USA ; Molecular and Cellular Biology Program, University of Washington Seattle, WA, USA ; Lawrence Berkeley National Lab Berkeley, CA, USA
| | | |
Collapse
|
85
|
Ellens KW, Richardson LGL, Frelin O, Collins J, Ribeiro CL, Hsieh YF, Mullen RT, Hanson AD. Evidence that glutamine transaminase and omega-amidase potentially act in tandem to close the methionine salvage cycle in bacteria and plants. PHYTOCHEMISTRY 2015; 113:160-169. [PMID: 24837359 DOI: 10.1016/j.phytochem.2014.04.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/07/2014] [Accepted: 04/12/2014] [Indexed: 06/03/2023]
Abstract
S-Adenosylmethionine is converted enzymatically and non-enzymatically to methylthioadenosine, which is recycled to methionine (Met) via a salvage pathway. In plants and bacteria, enzymes for all steps in this pathway are known except the last: transamination of α-ketomethylthiobutyrate to give Met. In mammals, glutamine transaminase K (GTK) and ω-amidase (ω-Am) are thought to act in tandem to execute this step, with GTK forming α-ketoglutaramate, which ω-Am hydrolyzes. Comparative genomics indicated that GTK and ω-Am could function likewise in plants and bacteria because genes encoding GTK and ω-Am homologs (i) co-express with the Met salvage gene 5-methylthioribose kinase in Arabidopsis, and (ii) cluster on the chromosome with each other and with Met salvage genes in diverse bacteria. Consistent with this possibility, tomato, maize, and Bacillus subtilis GTK and ω-Am homologs had the predicted activities: GTK was specific for glutamine as amino donor and strongly preferred α-ketomethylthiobutyrate as amino acceptor, and ω-Am strongly preferred α-ketoglutaramate. Also consistent with this possibility, plant GTK and ω-Am were localized to the cytosol, where the Met salvage pathway resides, as well as to organelles. This multiple targeting was shown to result from use of alternative start codons. In B. subtilis, ablating GTK or ω-Am had a modest but significant inhibitory effect on growth on 5-methylthioribose as sole sulfur source. Collectively, these data indicate that while GTK, coupled with ω-Am, is positioned to support significant Met salvage flux in plants and bacteria, it can probably be replaced by other aminotransferases.
Collapse
Affiliation(s)
- Kenneth W Ellens
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.
| | - Lynn G L Richardson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Joseph Collins
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Cintia Leite Ribeiro
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Yih-Feng Hsieh
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
86
|
Widhalm JR, Dudareva N. A familiar ring to it: biosynthesis of plant benzoic acids. MOLECULAR PLANT 2015; 8:83-97. [PMID: 25578274 DOI: 10.1016/j.molp.2014.12.001] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/19/2014] [Indexed: 05/20/2023]
Abstract
Plant benzoic acids (BAs) are building blocks or important structural elements for numerous primary and specialized metabolites, including plant hormones, cofactors, defense compounds, and attractants for pollinators and seed dispersers. Many natural products derived from plant BAs or containing benzoyl/benzyl moieties are also of medicinal or nutritional value to humans. Biosynthesis of BAs in plants is a network involving parallel and intersecting pathways spread across multiple subcellular compartments. In this review, a current overview on the metabolism of plant BAs is presented with a focus on the recent progress made on isolation and functional characterization of genes encoding biosynthetic enzymes and intracellular transporters. In addition, approaches for deciphering the complex interactions between pathways of the BAs network are discussed.
Collapse
Affiliation(s)
- Joshua R Widhalm
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN 47907-2063, USA.
| |
Collapse
|
87
|
Yang YS, Fernandez B, Lagorce A, Aloin V, De Guillen KM, Boyer JB, Dedieu A, Confalonieri F, Armengaud J, Roumestand C. Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans. Proteomics 2015; 15:114-23. [PMID: 25359407 DOI: 10.1002/pmic.201300535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 10/01/2014] [Accepted: 10/24/2014] [Indexed: 11/09/2022]
Abstract
ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions. Its solution structure has been determined using multidimensional heteronuclear NMR spectroscopy. TGAM_1934 displays an original fold, although sharing some similarities with the 3D structure of the bacterial ortholog of frataxin, CyaY, a protein conserved in bacteria and eukaryotes and involved in iron-sulfur cluster biogenesis. These results highlight the potential of structural proteomics in prioritizing ORFan targets for structure determination based on quantitative proteomics data. The proteomic data and structure coordinates have been deposited to the ProteomeXchange with identifier PXD000402 (http://proteomecentral.proteomexchange.org/dataset/PXD000402) and Protein Data Bank under the accession number 2mcf, respectively.
Collapse
Affiliation(s)
- Yin-Shan Yang
- Centre de Biochimie Structurale, Universités de Montpellier, Montpellier, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
88
|
Sulpice R, McKeown PC. Moving toward a comprehensive map of central plant metabolism. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:187-210. [PMID: 25621519 DOI: 10.1146/annurev-arplant-043014-114720] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Decades of intensive study have led to the discovery of the main pathways involved in central metabolism but only some of the pathways and regulatory networks in which they are embedded. In this review, we discuss techniques used to assemble these pathways into a systems biology framework that can enable accurate modeling of the response of central metabolism to changes, including ways to perturb metabolic systems and assemble the resulting data into a meaningful network. Critically, these networks are of such size and complexity that it is possible to derive them only if data from different groups can be comprehensively and meaningfully combined. We conclude that it is essential to establish common standards for the description of experimental conditions and data collection and to store this information in databases to which the whole community can contribute.
Collapse
|
89
|
Uvackova L, Ondruskova E, Danchenko M, Skultety L, Miernyk JA, Hrubík P, Hajduch M. Establishing a leaf proteome reference map for Ginkgo biloba provides insight into potential ethnobotanical uses. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:11547-11556. [PMID: 25365400 DOI: 10.1021/jf503375a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although ginkgo (Maidenhair tree, Ginkgo biloba L.) is an ancient medicinal and ornamental tree, there has not previously been any systematic proteomic study of the leaves. Herein we describe results from the initial study identifying abundant ginkgo leaf proteins and present a gel reference map. Proteins were isolated from fully developed mature leaves in biological triplicate and analyzed by two-dimensional electrophoresis plus tandem mass spectrometry. Using this approach, we were able to reproducibly quantify 190 abundant protein spots, from which 157 proteins were identified. Most of identified proteins are associated with the energy and protein destination/storage categories. The reference map provides a basis for understanding the accumulation of flavonoids and other phenolic compounds in mature leaves (e.g., identification of chalcone synthase, the first committed enzyme in flavonoid biosynthesis). We additionally detected several proteins of as yet unknown function. These proteins comprise a pool of potential targets that might be useful in nontraditional medical applications.
Collapse
Affiliation(s)
- Lubica Uvackova
- Department of Reproduction and Developmental Biology, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences , 950 07 Nitra, Slovakia
| | | | | | | | | | | | | |
Collapse
|
90
|
Plant-driven repurposing of the ancient S-adenosylmethionine repair enzyme homocysteine S-methyltransferase. Biochem J 2014; 463:279-86. [PMID: 25046177 DOI: 10.1042/bj20140753] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Homocysteine S-methyltransferases (HMTs) are widely distributed enzymes that convert homocysteine (Hcy) into methionine (Met) using either S-adenosylmethionine (AdoMet) or the plant secondary product S-methylmethionine (SMM) as methyl donor. AdoMet is chirally and covalently unstable, with racemization of natural (S,S)-AdoMet yielding biologically inactive (R,S)-AdoMet and depurination yielding S-ribosylmethionine (S-ribosylMet). The apparently futile AdoMet-dependent reaction of HMTs was assigned a role in repairing chiral damage to AdoMet in yeast: yeast HMTs strongly prefer (R,S)- to (S,S)-AdoMet and thereby limit (R,S)-AdoMet build-up [Vinci and Clarke (2010) J. Biol. Chem. 285, 20526-20531]. In the present study, we show that bacterial, plant, protistan and animal HMTs likewise prefer (R,S)- over (S,S)-AdoMet, that their ability to use SMM varies greatly and is associated with the likely prevalence of SMM in the environment of the organism and that most HMTs cannot use S-ribosylMet. Taken with results from comparative genomic and phylogenetic analyses, these data imply that (i) the ancestral function of HMTs was (R,S)-AdoMet repair, (ii) the efficient use of SMM reflects the repurposing of HMTs after the evolutionary advent of plants introduced SMM into the biosphere, (iii) this plant-driven repurposing was facile and occurred independently in various lineages, and (iv) HMTs have little importance in S-ribosylMet metabolism.
Collapse
|
91
|
Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V. GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. Nucleic Acids Res 2014; 43:D1010-7. [PMID: 25392409 PMCID: PMC4383956 DOI: 10.1093/nar/gku1155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein–protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17 264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource.
Collapse
Affiliation(s)
- Rim Zaag
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean Philippe Tamby
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Cécile Guichard
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Zakia Tariq
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Guillem Rigaill
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Etienne Delannoy
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean-Pierre Renou
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Sandrine Balzergue
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Tristan Mary-Huard
- INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France UMRGV, INRA, Université Paris-Sud, CNRS, F-91190 Gif-sur-Yvette, Paris, France
| | - Sébastien Aubourg
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Marie-Laure Martin-Magniette
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France
| | - Véronique Brunaud
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| |
Collapse
|
92
|
Guo X, Crawford JM. An atypical orphan carbohydrate-NRPS genomic island encodes a novel lytic transglycosylase. ACTA ACUST UNITED AC 2014; 21:1271-1277. [PMID: 25219963 DOI: 10.1016/j.chembiol.2014.07.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/19/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Microbial genome sequencing platforms have produced a deluge of orphan biosynthetic pathways suspected of biosynthesizing new small molecules with pharmacological relevance. Genome synteny analysis provides an assessment of genomic island content, which is enriched in natural product gene clusters. Here we identified an atypical orphan carbohydrate-nonribosomal peptide synthetase genomic island in Photorhabdus luminescens using genome synteny analysis. Heterologous expression of the pathway led to the characterization of five oligosaccharide metabolites with lysozyme inhibitory activities. The oligosaccharides harbor a 1,6-anhydro-β-D-N-acetyl-glucosamine moiety, a rare structural feature for natural products. Gene deletion analysis and biochemical reconstruction of oligosaccharide production led to the discovery that a hypothetical protein in the pathway is a lytic transglycosylase responsible for bicyclic sugar formation. The example presented here supports the notion that targeting select genomic islands with reduced reliance on known protein homologies could enhance the discovery of new metabolic chemistry and biology.
Collapse
Affiliation(s)
- Xun Guo
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
93
|
Hehemann JH, Boraston AB, Czjzek M. A sweet new wave: structures and mechanisms of enzymes that digest polysaccharides from marine algae. Curr Opin Struct Biol 2014; 28:77-86. [DOI: 10.1016/j.sbi.2014.07.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 10/24/2022]
|
94
|
Zallot R, Brochier-Armanet C, Gaston KW, Forouhar F, Limbach PA, Hunt JF, de Crécy-Lagard V. Plant, animal, and fungal micronutrient queuosine is salvaged by members of the DUF2419 protein family. ACS Chem Biol 2014; 9:1812-25. [PMID: 24911101 PMCID: PMC4136680 DOI: 10.1021/cb500278k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Queuosine (Q) is a modification found
at the wobble position of
tRNAs with GUN anticodons. Although Q is present in most eukaryotes
and bacteria, only bacteria can synthesize Q de novo. Eukaryotes acquire queuine (q), the free base of Q, from diet and/or
microflora, making q an important but under-recognized micronutrient
for plants, animals, and fungi. Eukaryotic type tRNA-guanine transglycosylases
(eTGTs) are composed of a catalytic subunit (QTRT1) and a homologous
accessory subunit (QTRTD1) forming a complex that catalyzes q insertion
into target tRNAs. Phylogenetic analysis of eTGT subunits revealed
a patchy distribution pattern in which gene losses occurred independently
in different clades. Searches for genes co-distributing with eTGT
family members identified DUF2419 as a potential Q salvage protein
family. This prediction was experimentally validated in Schizosaccharomyces
pombe by confirming that Q was present by analyzing tRNAAsp with anticodon GUC purified from wild-type cells and by
showing that Q was absent from strains carrying deletions in the QTRT1
or DUF2419 encoding genes. DUF2419 proteins occur in most Eukarya
with a few possible cases of horizontal gene transfer to bacteria.
The universality of the DUF2419 function was confirmed by complementing
the S. pombe mutant with the Zea mays (maize), human, and Sphaerobacter thermophilus homologues.
The enzymatic function of this family is yet to be determined, but
structural similarity with DNA glycosidases suggests a ribonucleoside
hydrolase activity.
Collapse
Affiliation(s)
- Rémi Zallot
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
| | - Céline Brochier-Armanet
- Université
Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie
Evolutive, Université de Lyon, 69622 Villeurbanne, France
| | - Kirk W. Gaston
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Farhad Forouhar
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Patrick A. Limbach
- Rieveschl
Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - John F. Hunt
- Department
of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Genetics Institute, Gainesville, Florida 32611, United States
| |
Collapse
|
95
|
Carrera J, Estrela R, Luo J, Rai N, Tsoukalas A, Tagkopoulos I. An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli. Mol Syst Biol 2014; 10:735. [PMID: 24987114 PMCID: PMC4299492 DOI: 10.15252/msb.20145108] [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] [Indexed: 11/10/2022] Open
Abstract
Given the vast behavioral repertoire and biological complexity of even the simplest organisms,
accurately predicting phenotypes in novel environments and unveiling their biological organization
is a challenging endeavor. Here, we present an integrative modeling methodology that unifies under a
common framework the various biological processes and their interactions across multiple layers. We
trained this methodology on an extensive normalized compendium for the gram-negative bacterium
Escherichia coli, which incorporates gene expression data for genetic and
environmental perturbations, transcriptional regulation, signal transduction, and metabolic
pathways, as well as growth measurements. Comparison with measured growth and high-throughput data
demonstrates the enhanced ability of the integrative model to predict phenotypic outcomes in various
environmental and genetic conditions, even in cases where their underlying functions are
under-represented in the training set. This work paves the way toward integrative techniques that
extract knowledge from a variety of biological data to achieve more than the sum of their parts in
the context of prediction, analysis, and redesign of biological systems.
Collapse
Affiliation(s)
- Javier Carrera
- UC Davis Genome Center, University of California, Davis, CA, USA
| | - Raissa Estrela
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Jing Luo
- UC Davis Genome Center, University of California, Davis, CA, USA
| | - Navneet Rai
- UC Davis Genome Center, University of California, Davis, CA, USA
| | - Athanasios Tsoukalas
- UC Davis Genome Center, University of California, Davis, CA, USA Department of Computer Science, University of California, Davis, CA, USA
| | - Ilias Tagkopoulos
- UC Davis Genome Center, University of California, Davis, CA, USA Department of Computer Science, University of California, Davis, CA, USA
| |
Collapse
|
96
|
El Yacoubi B, de Crécy-Lagard V. Integrative data-mining tools to link gene and function. Methods Mol Biol 2014; 1101:43-66. [PMID: 24233777 DOI: 10.1007/978-1-62703-721-1_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Information derived from genomic and post-genomic data can be efficiently used to link gene and function. Several web-based platforms have been developed to mine these types of data by integrating different tools. This method paper is designed to allow the user to navigate these platforms in order to make functional predictions. The main focus is on phylogenetic distribution and physical clustering tools, but other tools such as pathway reconstruction, gene fusions, and analysis of high-throughput experimental data are also surveyed.
Collapse
Affiliation(s)
- Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | | |
Collapse
|
97
|
Trichler SA, Bulla SC, Mahajan N, Lunsford KV, Pendarvis K, Nanduri B, McCarthy FM, Bulla C. Identification of canine platelet proteins separated by differential detergent fractionation for nonelectrophoretic proteomics analyzed by Gene Ontology and pathways analysis. VETERINARY MEDICINE-RESEARCH AND REPORTS 2014; 5:1-9. [PMID: 32670841 PMCID: PMC7337207 DOI: 10.2147/vmrr.s47127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/23/2014] [Indexed: 01/20/2023]
Abstract
During platelet development, proteins necessary for the many functional roles of the platelet are stored within cytoplasmic granules. Platelets have also been shown to take up and store many plasma proteins into granules. This makes the platelet a potential novel source of biomarkers for many disease states. Approaches to sample preparation for proteomic studies for biomarkers search vary. Compared with traditional two-dimensional polyacrylamide gel electrophoresis systems, nonelectrophoretic proteomics methods that employ offline protein fractionation methods such as the differential detergent fractionation method have clear advantages. Here we report a proteomic survey of the canine platelet proteome using differential detergent fractionation coupled with mass spectrometry and functional modeling of the canine platelet proteins identified. A total of 5,974 unique proteins were identified from platelets, of which only 298 (5%) had previous experimental evidence of in vivo expression. The use of offline prefractionation of canine proteins by differential detergent fractionation resulted in greater proteome coverage as compared with previous reports. This initial study contributes to a broader understanding of canine platelet biology and aids functional research, identification of potential treatment targets and biomarkers, and sets a new standard for the resting platelet proteome.
Collapse
Affiliation(s)
| | | | | | - Kari V Lunsford
- Department of Clinical Sciences and Animal Health Center, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS
| | - Ken Pendarvis
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ
| | - Bindu Nanduri
- Department of Biological Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS.,Institute for Genomics, Biocomputing and Biotechnology, Starkville, MS, USA
| | - Fiona M McCarthy
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ
| | - Camilo Bulla
- Department of Pathobiology and Population Medicine
| |
Collapse
|
98
|
de Crécy-Lagard V. Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. Comput Struct Biotechnol J 2014; 10:41-50. [PMID: 25210598 PMCID: PMC4151868 DOI: 10.1016/j.csbj.2014.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The availability of thousands of sequenced genomes has revealed the diversity of biochemical solutions to similar chemical problems. Even for molecules at the heart of metabolism, such as cofactors, the pathway enzymes first discovered in model organisms like Escherichia coli or Saccharomyces cerevisiae are often not universally conserved. Tetrahydrofolate (THF) (or its close relative tetrahydromethanopterin) is a universal and essential C1-carrier that most microbes and plants synthesize de novo. The THF biosynthesis pathway and enzymes are, however, not universal and alternate solutions are found for most steps, making this pathway a challenge to annotate automatically in many genomes. Comparing THF pathway reconstructions and functional annotations of a chosen set of folate synthesis genes in specific prokaryotes revealed the strengths and weaknesses of different microbial annotation platforms. This analysis revealed that most current platforms fail in metabolic reconstruction of variant pathways. However, all the pieces are in place to quickly correct these deficiencies if the different databases were built on each other's strengths.
Collapse
Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science and Genetics Institute, University of Florida, Gainesville, FL, United States
| |
Collapse
|
99
|
Sorokina M, Stam M, Médigue C, Lespinet O, Vallenet D. Profiling the orphan enzymes. Biol Direct 2014; 9:10. [PMID: 24906382 PMCID: PMC4084501 DOI: 10.1186/1745-6150-9-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/29/2014] [Indexed: 11/10/2022] Open
Abstract
The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called "orphan enzymes". The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to "local orphan enzymes" that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new activities.
Collapse
Affiliation(s)
- Maria Sorokina
- Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France.
| | | | | | | | | |
Collapse
|
100
|
Islam MA, Waller AS, Hug LA, Provart NJ, Edwards EA, Mahadevan R. New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PLoS One 2014; 9:e94808. [PMID: 24733489 PMCID: PMC3986231 DOI: 10.1371/journal.pone.0094808] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/19/2014] [Indexed: 12/16/2022] Open
Abstract
Organohalide respiration, mediated by Dehalococcoides mccartyi, is a useful bioremediation process that transforms ground water pollutants and known human carcinogens such as trichloroethene and vinyl chloride into benign ethenes. Successful application of this process depends on the fundamental understanding of the respiration and metabolism of D. mccartyi. Reductive dehalogenases, encoded by rdhA genes of these anaerobic bacteria, exclusively catalyze organohalide respiration and drive metabolism. To better elucidate D. mccartyi metabolism and physiology, we analyzed available transcriptomic data for a pure isolate (Dehalococcoides mccartyi strain 195) and a mixed microbial consortium (KB-1) using the previously developed pan-genome-scale reconstructed metabolic network of D. mccartyi. The transcriptomic data, together with available proteomic data helped confirm transcription and expression of the majority genes in D. mccartyi genomes. A composite genome of two highly similar D. mccartyi strains (KB-1 Dhc) from the KB-1 metagenome sequence was constructed, and operon prediction was conducted for this composite genome and other single genomes. This operon analysis, together with the quality threshold clustering analysis of transcriptomic data helped generate experimentally testable hypotheses regarding the function of a number of hypothetical proteins and the poorly understood mechanism of energy conservation in D. mccartyi. We also identified functionally enriched important clusters (13 for strain 195 and 11 for KB-1 Dhc) of co-expressed metabolic genes using information from the reconstructed metabolic network. This analysis highlighted some metabolic genes and processes, including lipid metabolism, energy metabolism, and transport that potentially play important roles in organohalide respiration. Overall, this study shows the importance of an organism's metabolic reconstruction in analyzing various "omics" data to obtain improved understanding of the metabolism and physiology of the organism.
Collapse
Affiliation(s)
- M. Ahsanul Islam
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alison S. Waller
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Laura A. Hug
- Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America
| | - Nicholas J. Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|