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Guo H, Lei T, Yang J, Wang Y, Wang Y, Ji Y. New Insights into the Biological Functions of Essential TsaB/YeaZ Protein in Staphylococcus aureus. Antibiotics (Basel) 2024; 13:393. [PMID: 38786122 PMCID: PMC11117223 DOI: 10.3390/antibiotics13050393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
TsaB/YeaZ represents a promising target for novel antibacterial agents due to its indispensable role in bacterial survival, high conservation within bacterial species, and absence of eukaryotic homologs. Previous studies have elucidated the role of the essential staphylococcal protein, TsaB/YeaZ, in binding DNA to mediate the transcription of the ilv-leu operon, responsible for encoding key enzymes involved in the biosynthesis of branched-chain amino acids-namely isoleucine, leucine, and valine (ILV). However, the regulation of ILV biosynthesis does not account for the essentiality of TsaB/YeaZ for bacterial growth. In this study, we investigated the impact of TsaB/YeaZ depletion on bacterial morphology and gene expression profiles using electron microscopy and deep transcriptomic analysis, respectively. Our results revealed significant alterations in bacterial size and surface smoothness upon TsaB/YeaZ depletion. Furthermore, we pinpointed specific genes and enriched biological pathways significantly affected by TsaB/YeaZ during the early and middle exponential phases and early stationary phases of growth. Crucially, our research uncovered a regulatory role for TsaB/YeaZ in bacterial autolysis. These discoveries offer fresh insights into the multifaceted biological functions of TsaB/YeaZ within S. aureus.
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Affiliation(s)
- Haiyong Guo
- School of Life Science, Jilin Normal University, Siping 136000, China; (H.G.)
| | - Ting Lei
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (T.L.)
| | - Junshu Yang
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (T.L.)
| | - Yue Wang
- School of Life Science, Jilin Normal University, Siping 136000, China; (H.G.)
| | - Yifan Wang
- School of Life Science, Jilin Normal University, Siping 136000, China; (H.G.)
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA; (T.L.)
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2
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Boteva E, Doychev K, Kirilov K, Handzhiyski Y, Tsekovska R, Gatev E, Mironova R. Deglycation activity of the Escherichia coli glycolytic enzyme phosphoglucose isomerase. Int J Biol Macromol 2024; 257:128541. [PMID: 38056730 DOI: 10.1016/j.ijbiomac.2023.128541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Glycation is a spontaneous chemical reaction, which affects the structure and function of proteins under normal physiological conditions. Therefore, organisms have evolved diverse mechanisms to combat glycation. In this study, we show that the Escherichia coli glycolytic enzyme phosphoglucose isomerase (Pgi) exhibits deglycation activity. We found that E. coli Pgi catalyzes the breakdown of glucose 6-phosphate (G6P)-derived Amadori products (APs) in chicken lysozyme. The affinity of Pgi to the glycated lysozyme (Km, 1.1 mM) was ten times lower than the affinity to its native substrate, fructose 6-phosphate (Km, 0.1 mM). However, the high kinetic constants of the enzyme with the glycated lysozyme (kcat, 396 s-1 and kcat/Km, 3.6 × 105 M-1 s-1) indicated that the Pgi amadoriase activity may have physiological implications. Indeed, when using total E. coli protein (20 mg/mL) as a substrate in the deglycation reaction, we observed a release of G6P from the bacterial protein at a Pgi specific activity of 33 μmol/min/mg. Further, we detected 11.4 % lower APs concentration in protein extracts from Pgi-proficient vs. deficient cells (p = 0.0006) under conditions where the G6P concentration in Pgi-proficient cells was four times higher than in Pgi-deficient cells (p = 0.0001). Altogether, these data point to physiological relevance of the Pgi deglycation activity.
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Affiliation(s)
- Elitsa Boteva
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Konstantin Doychev
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Kiril Kirilov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Yordan Handzhiyski
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Rositsa Tsekovska
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Evan Gatev
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
| | - Roumyana Mironova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria.
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3
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Mossine VV, Mawhinney TP. 1-Amino-1-deoxy-d-fructose ("fructosamine") and its derivatives: An update. Adv Carbohydr Chem Biochem 2023; 83:1-26. [PMID: 37968036 DOI: 10.1016/bs.accb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
1-Amino-1-deoxy-d-fructose (fructosamine, FN) derivatives are omnipresent in all living organisms, as a result of non-enzymatic condensation and Amadori rearrangement reactions between free glucose and biogenic amines such as amino acids, polypeptides, or aminophospholipids. Over decades, steady interest in fructosamine was largely sustained by its role as a key intermediate structure in the Maillard reaction that is responsible for the organoleptic and nutritional value of thermally processed foods, and for pathophysiological effects of hyperglycemia in diabetes. New trends in fructosamine research include the discovery and engineering of FN-processing enzymes, development of advanced tools for hyperglycemia monitoring, and evaluation of the therapeutic potential of both fructosamines and FN-recognizing proteins. This article covers developments in the field of fructosamine and its derivatives since 2010 and attempts to ascertain challenges in future research.
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Affiliation(s)
- Valeri V Mossine
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Thomas P Mawhinney
- Department of Biochemistry, University of Missouri, Columbia, MO, United States.
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4
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de Crécy-Lagard V, Jaroch M. Functions of Bacterial tRNA Modifications: From Ubiquity to Diversity. Trends Microbiol 2020; 29:41-53. [PMID: 32718697 DOI: 10.1016/j.tim.2020.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 01/21/2023]
Abstract
Modified nucleotides in tRNA are critical components of the translation apparatus, but their importance in the process of translational regulation had until recently been greatly overlooked. Two breakthroughs have recently allowed a fuller understanding of the importance of tRNA modifications in bacterial physiology. One is the identification of the full set of tRNA modification genes in model organisms such as Escherichia coli K12. The second is the improvement of available analytical tools to monitor tRNA modification patterns. The role of tRNA modifications varies greatly with the specific modification within a given tRNA and with the organism studied. The absence of these modifications or reductions can lead to cell death or pleiotropic phenotypes or may have no apparent visible effect. By linking translation through their decoding functions to metabolism through their biosynthetic pathways, tRNA modifications are emerging as important components of the bacterial regulatory toolbox.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
| | - Marshall Jaroch
- Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA
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5
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Zhang Y, Chen J, Wang Y, Li Y, Rui W, Zhang J, Luo D. Expression and protease characterization of a conserved protein YgjD in Vibrio harveyi. PeerJ 2020; 8:e9061. [PMID: 32477834 PMCID: PMC7241418 DOI: 10.7717/peerj.9061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/04/2020] [Indexed: 11/20/2022] Open
Abstract
The glycopeptidase GCP and its homologue proteins are conserved and essential for survival of bacteria. The ygjD gene (Glycopeptidase homologue) was cloned from Vibrio harveyi strain SF-1. The gene consisted of 1,017 bp, which encodes a 338 amino acid polypeptide. The nucleotide sequence similarity of the ygjD gene with that of V. harveyi FDAARGOS 107 was 95%. The ygjD gene also showed similarities of 68%, 67% and 50% with those of Salmonella enterica, Escherichia coli and Bacillus cereus. The ygjD gene was expressed in E. coli BL21 (DE3) and the recombinant YgjD was purified by Ni2+ affinity chromatography column. The purified YgjD showed a specific 37 kDa band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and exhibited protease activities of 59,000 units/mg, 53,700 units/mg and 8,100 units/mg, respectively, on N-Acetyl-L-tyrosine ethyl ester monohydrate (ATEE), N-Benzoyl-L-tyrosine ethyl ester (BTEE) and N-Benzoyl-DL-arginine-4-nitroanilide hydrochloride (BAPNA) substrates. When the conserved amino acids of His111, Glu113 and His115 in the YgjD were replaced with alanine, respectively, the protease activities of the mutants were partly decreased. The two conserved His111 and His115 of YgjD were mutated and the protein lost the protease activity, which implied that the two amino acid played very important roles in maintaining its protease activity. The addition of the purified YgjD to the culture medium of V. harveyi strain SF-1 can effectively promote the bacteria growth. These results indicated that the protease activities may be involved in the survival of bacteria.
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Affiliation(s)
- Yayuan Zhang
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Jixiang Chen
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Yonggang Wang
- School of life science and enginerring, Lanzhou University of Technology, Lanzhou, China
| | - Yanlin Li
- Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences, Chongqing, China
| | - Wenhong Rui
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Jiyi Zhang
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
| | - Dan Luo
- School of Petrochemical Engineering, Lanzhou University of Technology, Lanzhou, China
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6
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Britton TA, Guo H, Ji Y. Interaction between two essential, conserved bacterial proteins YeaZ and glycoprotease as a potential antibacterial target in multi-drug-resistant Staphylococcus aureus. Sci Prog 2020; 103:36850419890521. [PMID: 31829791 PMCID: PMC10452758 DOI: 10.1177/0036850419890521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein-protein interactions among highly conserved and essential proteins can serve as new targets for antibacterial therapies. One protein-protein interaction between two widely conserved and essential bacterial proteins, YeaZ and its paralog, a putative glycoprotease, is being looked into for its antimicrobial drug potential. These two proteins possess tandem functions, including repression of the branched-chain amino acids biosynthesis and induction of a tRNA modification important in enhancing translation fidelity through anticodon-codon base pairing. Heterodimer formation between these two proteins is essential for Staphylococcus aureus, and other bacterial species including Escherichia coli and Salmonella typhimurium. Such YeaZ-glycoprotease interaction could thus be a target for antimicrobial drugs designed for multi-drug-resistant S. aureus. In this review, we discuss the function, structure, and interaction between these two proteins and their orthologs in other bacteria.
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Affiliation(s)
- Timmie A Britton
- College of Biomedical Science, University of Minnesota, Minneapolis, MN, USA
| | - Haiyong Guo
- College of Life Science, Jilin Normal University, Siping, China
| | - Yinduo Ji
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Minneapolis, MN, USA
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7
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Sillner N, Walker A, Hemmler D, Bazanella M, Heinzmann SS, Haller D, Schmitt-Kopplin P. Milk-Derived Amadori Products in Feces of Formula-Fed Infants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8061-8069. [PMID: 31264412 DOI: 10.1021/acs.jafc.9b01889] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Food processing of infant formula alters chemical structures, including the formation of Maillard reaction products between proteins and sugars. We detected early Maillard reaction products, so-called Amadori products, in stool samples of formula-fed infants. In total, four Amadori products (N-deoxylactulosyllysine, N-deoxyfructosyllysine, N-deoxylactulosylleucylisoleucine, N-deoxyfructosylleucylisoleucine) were identified by a combination of complementary nontargeted and targeted metabolomics approaches. Chemical structures were confirmed by preparation and isolation of reference compounds, LC-MS/MS, and NMR. The leucylisoleucine Amadori compounds, which most likely originate from β-lactoglobulin, were excreted throughout the first year of life in feces of formula-fed infants but were absent in feces of breastfed infants. Despite high inter- and intraindividual differences of Amadori products in the infants' stool, solid food introduction resulted in a continuous decrease, proving infant formula as the major source of the excreted Amadori products.
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Affiliation(s)
- Nina Sillner
- Research Unit Analytical BioGeoChemistry , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- ZIEL Institute for Food and Health , Technical University of Munich , 85354 Freising , Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Daniel Hemmler
- Research Unit Analytical BioGeoChemistry , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- Chair of Analytical Food Chemistry , Technical University of Munich , 85354 Freising , Germany
| | - Monika Bazanella
- Chair of Nutrition and Immunology , Technical University of Munich , 85354 Freising , Germany
| | - Silke S Heinzmann
- Research Unit Analytical BioGeoChemistry , Helmholtz Zentrum München , 85764 Neuherberg , Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health , Technical University of Munich , 85354 Freising , Germany
- Chair of Nutrition and Immunology , Technical University of Munich , 85354 Freising , Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry , Helmholtz Zentrum München , 85764 Neuherberg , Germany
- ZIEL Institute for Food and Health , Technical University of Munich , 85354 Freising , Germany
- Chair of Analytical Food Chemistry , Technical University of Munich , 85354 Freising , Germany
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8
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Ogura M, Sato T, Abe K. Bacillus subtilis YlxR, Which Is Involved in Glucose-Responsive Metabolic Changes, Regulates Expression of tsaD for Protein Quality Control of Pyruvate Dehydrogenase. Front Microbiol 2019; 10:923. [PMID: 31118925 PMCID: PMC6504816 DOI: 10.3389/fmicb.2019.00923] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/11/2019] [Indexed: 01/09/2023] Open
Abstract
Glucose is the most favorable carbon source for many bacteria, which have several glucose-responsive gene networks. Recently, we found that in Bacillus subtilis glucose induces the expression of the extracellular sigma factor genes sigX and sigM through the acetylation of CshA (RNA helicase), which associates with RNA polymerase (RNAP). We performed a transposon mutagenesis screen for mutants with no glucose induction (GI) of sigX-lacZ. While screening for such mutants, we recently found that the GI of sigX/M involves YlxR, a nucleoid-associated protein (NAP) that regulates nearly 400 genes, including metabolic genes. It has been shown that acetylated CshA positively regulates expression of ylxR-containing operon. Here, we report additional mutations in yqfO or tsaD required for the GI of sigX. YqfO contains a universally conserved domain with unknown function. YqfO and YlxR were found to regulate expression of the tsaEBD-containing operon. Mutational analysis using lacZ fusions revealed the adenine-rich cis-element for YlxR. TsaD is a component of the TsaEBD enzyme required for the synthesis of threonylcarbamoyl adenosine (t6A). The t6A modification of tRNA is universal across the three domains of life. Western blot analysis showed that the tsaD mutation in the presence of glucose reduced levels of soluble PdhA, PdhB, and PdhD, which are subunits of the pyruvate dehydrogenase complex (PDHc). This resulted in severely defective PDHc function and thus reduced concentrations of cellular acetyl-CoA, a reaction product of PDHc and plausible source for CshA acetylation. Thus, we discuss a suggested glucose-responsive system (GRS) involving self-reinforcing CshA acetylation. This self-reinforcing pathway may contribute to the maintenance of the acetyl-CoA pool for protein acetylation.
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Affiliation(s)
- Mitsuo Ogura
- Institute of Oceanic Research and Development, Tokai University, Shizuoka, Japan
| | - Tsutomu Sato
- Department of Frontier Bioscience, Hosei University, Koganei, Japan
| | - Kimihiro Abe
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
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9
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Boteva E, Mironova R. Maillard reaction and aging: can bacteria shed light on the link? BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1590160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Elitsa Boteva
- Department of Gene Regulation, Institute of Molecular Biology ‘Roumen Tsanev’, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Roumyana Mironova
- Department of Gene Regulation, Institute of Molecular Biology ‘Roumen Tsanev’, Bulgarian Academy of Sciences, Sofia, Bulgaria
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10
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Thiaville PC, Legendre R, Rojas-Benítez D, Baudin-Baillieu A, Hatin I, Chalancon G, Glavic A, Namy O, de Crécy-Lagard V. Global translational impacts of the loss of the tRNA modification t 6A in yeast. MICROBIAL CELL 2016; 3:29-45. [PMID: 26798630 PMCID: PMC4717488 DOI: 10.15698/mic2016.01.473] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The universal tRNA modification t6A is found at position 37 of nearly
all tRNAs decoding ANN codons. The absence of t6A37 leads
to severe growth defects in baker’s yeast, phenotypes similar to those caused by
defects in mcm5s2U34 synthesis. Mutants in
mcm5s2U34 can be suppressed by
overexpression of tRNALysUUU, but we show t6A
phenotypes could not be suppressed by expressing any individual ANN decoding
tRNA, and t6A and mcm5s2U are not determinants
for each other’s formation. Our results suggest that t6A deficiency,
like mcm5s2U deficiency, leads to protein folding defects,
and show that the absence of t6A led to stress sensitivities (heat,
ethanol, salt) and sensitivity to TOR pathway inhibitors. Additionally,
L-homoserine suppressed the slow growth phenotype seen in
t6A-deficient strains, and proteins aggregates and Advanced Glycation
End-products (AGEs) were increased in the mutants. The global consequences on
translation caused by t6A absence were examined by ribosome
profiling. Interestingly, the absence of t6A did not lead to global
translation defects, but did increase translation initiation at upstream non-AUG
codons and increased frame-shifting in specific genes. Analysis of codon
occupancy rates suggests that one of the major roles of t6A is to
homogenize the process of elongation by slowing the elongation rate at codons
decoded by high abundance tRNAs and I34:C3 pairs while
increasing the elongation rate of rare tRNAs and G34:U3
pairs. This work reveals that the consequences of t6A absence are
complex and multilayered and has set the stage to elucidate the molecular basis
of the observed phenotypes.
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Affiliation(s)
- Patrick C Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL 32610, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Rachel Legendre
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Diego Rojas-Benítez
- Centro de Regulación del Genoma. Facultad de Ciencias - Universidad de Chile, Santiago, Chile
| | - Agnès Baudin-Baillieu
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Isabelle Hatin
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Guilhem Chalancon
- Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Alvaro Glavic
- Centro de Regulación del Genoma. Facultad de Ciencias - Universidad de Chile, Santiago, Chile
| | - Olivier Namy
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Sud, Bâtiment 400, 91400 Orsay, France
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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11
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Gil R, Peretó J. Small genomes and the difficulty to define minimal translation and metabolic machineries. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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12
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Thiaville PC, El Yacoubi B, Köhrer C, Thiaville JJ, Deutsch C, Iwata-Reuyl D, Bacusmo JM, Armengaud J, Bessho Y, Wetzel C, Cao X, Limbach PA, RajBhandary UL, de Crécy-Lagard V. Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria. Mol Microbiol 2015; 98:1199-221. [PMID: 26337258 DOI: 10.1111/mmi.13209] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 02/06/2023]
Abstract
Threonylcarbamoyladenosine (t(6)A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t(6)A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t(6)A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNA(Ile)-lysidine synthetase. We confirm that t(6)A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t(6)A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t(6)A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t(6)A(-) D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t(6)A in tRNAs. Thus, although t(6)A is universally conserved in tRNAs, its role in translation might vary greatly between organisms.
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Affiliation(s)
- Patrick C Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,Genetics and Genomics Graduate Program, University of Florida, Gainesville, FL, 32610, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.,Institut de Génétique et Microbiologie, Université of Paris-Sud, Orsay, France
| | - Basma El Yacoubi
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jennifer J Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Chris Deutsch
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, Portland State University, Portland, OR, 97297, USA
| | - Jo Marie Bacusmo
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Innovative technologies for Detection and Diagnostics', Bagnols-sur-Cèze, F-30200, France
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Institute of Physics, Academia Sinica, 128 Sec. 2, Academia Rd., Nankang, Taipei, 11529, Taiwan
| | - Collin Wetzel
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Xiaoyu Cao
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, 45221, USA
| | - Uttam L RajBhandary
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA.,University of Florida Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
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13
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Szwergold BS. Maillard reactions in hyperthermophilic archaea: implications for better understanding of non-enzymatic glycation in biology. Rejuvenation Res 2014; 16:259-72. [PMID: 23634960 DOI: 10.1089/rej.2012.1401] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Maillard reactions are an unavoidable feature of life that appear to be damaging to cell and organisms. Consequently, all living systems must have ways to protect themselves against this process. As of 2012, several such defense mechanisms have been identified. They are all enzymatic and were found in mesophilic organisms. To date, no systematic study of Maillard reactions and the relevant defense mechanisms has been conducted in thermophiles (50°C-80°C) or hyperthermophiles (80°C-120°C). This is surprisingly because Maillard reactions become significantly faster and potent with increasing temperatures. This review examines this neglected issue in two well-defined sets of hyperthermophiles. My analysis suggests that hyperthermophiles cope with glycation stress by several mechanisms: • Absence of glycation-prone head groups (such as ethanoalamine) from hyperthermophilic phospholipids • Protection of reactive carbohydrates and labile metabolic intermediates by substrate channeling. • Conversion of excess reactive sugars such as glucose to non-reactive compounds including trehalose, di-myo-inositol-phosphate and mannosylglycerate. • Detoxification of methylglyoxal and other ketoaldehydes by conversion to inert products through a variety of reductases and dehydrogenases. • Scavenging of the remaining carbonyls by nucleophilic amines, including a variety of novel polyamines. Disruption of the Maillard process at its early stages, rather than repair of damage caused by it at later stages, appears to be the preferred strategy in the organisms examined. The most unique among these mechanisms appears to be a polyamine-based scavenging system. Undertaking research of the Maillard process in hyperthermophiles is important in its own right and is also likely to provide new insights for the control of these reactions in humans, especially in diseases such as diabetes mellitus.
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Cohen-Or I, Katz C, Ron EZ. Metabolism of AGEs--bacterial AGEs are degraded by metallo-proteases. PLoS One 2013; 8:e74970. [PMID: 24130678 PMCID: PMC3794025 DOI: 10.1371/journal.pone.0074970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 08/12/2013] [Indexed: 11/19/2022] Open
Abstract
Advanced Glycation End Products (AGEs) are the final products of non-enzymatic protein glycation that results in loss of protein structure and function. We have previously shown that in E. coli AGEs are continually formed as high-molecular weight protein complexes. Moreover, we showed that AGEs are removed from the cells by an active, ATP-dependent secretion and that these secreted molecules have low molecular weight. Taken together, these results indicate that E. coli contains a fraction of low molecular weight AGEs, in addition to the high-molecular weight AGEs. Here we show that the low-molecular weight AGEs originate from high-molecular weight AGEs by proteolytic degradation. Results of in-vitro and in vivo experiments indicated that this degradation is carried out not by the major ATP-dependent proteases that are responsible for the main part of bacterial protein quality control but by an alternative metal-dependent proteolysis. This proteolytic reaction is essential for the further secretion of AGEs from the cells. As the biochemical reactions involving AGEs are not yet understood, the implication of a metalloprotease in breakdown of high molecular weight AGEs and their secretion constitutes an important step in the understanding of AGEs metabolism.
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Affiliation(s)
- Ifat Cohen-Or
- Department of Molecular Microbiology and Biotechnology, Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Chen Katz
- MIGAL – Galilee Research Center, Kiriat Shmone, Israel
| | - Eliora Z. Ron
- Department of Molecular Microbiology and Biotechnology, Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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Nichols CE, Lamb HK, Thompson P, El Omari K, Lockyer M, Charles I, Hawkins AR, Stammers DK. Crystal structure of the dimer of two essential Salmonella typhimurium proteins, YgjD & YeaZ and calorimetric evidence for the formation of a ternary YgjD-YeaZ-YjeE complex. Protein Sci 2013; 22:628-40. [PMID: 23471679 DOI: 10.1002/pro.2247] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/22/2013] [Accepted: 03/01/2013] [Indexed: 11/07/2022]
Abstract
YgjD from COG0533 is amongst a small group of highly conserved proteins present in all three domains of life. Various roles and biochemical functions (including sialoprotease and endonuclease activities) have been ascribed to YgjD and orthologs, the most recent, however, is involvement in the post transcriptional modification of certain tRNAs by formation of N6-threonyl-adenosine (t⁶A) at position 37. In bacteria, YgjD is essential and along with YeaZ, YjeE, and YrdC has been shown to be 'necessary and sufficient' for the tRNA modification. To further define interactions and possible roles for some of this set of proteins we have undertaken structural and biochemical studies. We show that formation of the previously reported heterodimer of YgjD-YeaZ involves ordering of the C-terminal region of YeaZ which extends along the surface of YgjD in the crystal structure. ATPγS or AMP is observed in YgjD while no nucleotide is bound on YeaZ. ITC experiments reveal previously unreported binary and ternary complexes which can be nucleotide dependent. The stoichiometry of the YeaZ-YgjD complex is 1:1 with a K(D) of 0.3 µM. YgjD and YjeE interact only in the presence of ATP, while YjeE binds to YgjD-YeaZ in the presence of ATP or ADP with a K(D) of 6 µM. YgjD doesn't bind the precursors of t⁶A, threonine, and bicarbonate. These results show a more complex set of interactions than previously thought, which may have a regulatory role. The understanding gained should help in deriving inhibitors of these essential proteins that might have potential as antibacterial drugs.
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Affiliation(s)
- C E Nichols
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom
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16
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Onodera T, Satoh K, Ohta T, Narumi I. Deinococcus radiodurans YgjD and YeaZ are involved in the repair of DNA cross-links. Extremophiles 2012; 17:171-9. [DOI: 10.1007/s00792-012-0506-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/29/2012] [Indexed: 12/29/2022]
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17
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Naor A, Thiaville PC, Altman-Price N, Cohen-Or I, Allers T, de Crécy-Lagard V, Gophna U. A genetic investigation of the KEOPS complex in halophilic Archaea. PLoS One 2012; 7:e43013. [PMID: 22927945 PMCID: PMC3426518 DOI: 10.1371/journal.pone.0043013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 07/17/2012] [Indexed: 12/01/2022] Open
Abstract
KEOPS is an important cellular complex conserved in Eukarya, with some subunits conserved in Archaea and Bacteria. This complex was recently found to play an essential role in formation of the tRNA modification threonylcarbamoyladenosine (t6A), and was previously associated with telomere length maintenance and transcription. KEOPS subunits are conserved in Archaea, especially in the Euryarchaea, where they had been studied in vitro. Here we attempted to delete the genes encoding the four conserved subunits of the KEOPS complex in the euryarchaeote Haloferax volcanii and study their phenotypes in vivo. The fused kae1-bud32 gene was shown to be essential as was cgi121, which is dispensable in yeast. In contrast, pcc1 (encoding the putative dimerizing unit of KEOPS) was not essential in H. volcanii. Deletion of pcc1 led to pleiotropic phenotypes, including decreased growth rate, reduced levels of t6A modification, and elevated levels of intra-cellular glycation products.
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Affiliation(s)
- Adit Naor
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Patrick C. Thiaville
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Neta Altman-Price
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ifat Cohen-Or
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Thorsten Allers
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (VdC); (UG)
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (VdC); (UG)
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18
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Deutsch C, El Yacoubi B, de Crécy-Lagard V, Iwata-Reuyl D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem 2012; 287:13666-73. [PMID: 22378793 DOI: 10.1074/jbc.m112.344028] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The anticodon stem-loop (ASL) of transfer RNAs (tRNAs) drives decoding by interacting directly with the mRNA through codon/anticodon pairing. Chemically complex nucleoside modifications found in the ASL at positions 34 or 37 are known to be required for accurate decoding. Although over 100 distinct modifications have been structurally characterized in tRNAs, only a few are universally conserved, among them threonylcarbamoyl adenosine (t(6)A), found at position 37 in the anticodon loop of a subset of tRNA. Structural studies predict an important role for t(6)A in translational fidelity, and in vivo work supports this prediction. Although pioneering work in the 1970s identified the fundamental substrates for t(6)A biosynthesis, the enzymes responsible for its biosynthesis have remained an enigma. We report here the discovery that in bacteria four proteins (YgjD, YrdC, YjeE, and YeaZ) are both necessary and sufficient for t(6)A biosynthesis in vitro. Notably, YrdC and YgjD are members of universally conserved families that were ranked among the top 10 proteins of unknown function in need of functional characterization, while YeaZ and YjeE are specific to bacteria. This latter observation, coupled with the essentiality of all four proteins in bacteria, establishes this pathway as a compelling new target for antimicrobial development.
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Affiliation(s)
- Christopher Deutsch
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
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Bergmiller T, Peña-Miller R, Boehm A, Ackermann M. Single-cell time-lapse analysis of depletion of the universally conserved essential protein YgjD. BMC Microbiol 2011; 11:118. [PMID: 21619589 PMCID: PMC3115834 DOI: 10.1186/1471-2180-11-118] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 05/27/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The essential Escherichia coli gene ygjD belongs to a universally conserved group of genes whose function has been the focus of a number of recent studies. Here, we put ygjD under control of an inducible promoter, and used time-lapse microscopy and single cell analysis to investigate the phenotypic consequences of the depletion of YgjD protein from growing cells. RESULTS We show that loss of YgjD leads to a marked decrease in cell size and termination of cell division. The transition towards smaller size occurs in a controlled manner: cell elongation and cell division remain coupled, but cell size at division decreases. We also find evidence that depletion of YgjD leads to the synthesis of the intracellular signaling molecule (p)ppGpp, inducing a cellular reaction resembling the stringent response. Concomitant deletion of the relA and spoT genes - leading to a strain that is uncapable of synthesizing (p)ppGpp - abrogates the decrease in cell size, but does not prevent termination of cell division upon YgjD depletion. CONCLUSIONS Depletion of YgjD protein from growing cells leads to a decrease in cell size that is contingent on (p)ppGpp, and to a termination of cell division. The combination of single-cell timelapse microscopy and statistical analysis can give detailed insights into the phenotypic consequences of the loss of essential genes, and can thus serve as a new tool to study the function of essential genes.
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Affiliation(s)
- Tobias Bergmiller
- Department of Environmental Sciences, ETH Zurich, Switzerland, and Department of Environmental Microbiology, Eawag, Switzerland.
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AGEs secreted by bacteria are involved in the inflammatory response. PLoS One 2011; 6:e17974. [PMID: 21445354 PMCID: PMC3062560 DOI: 10.1371/journal.pone.0017974] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 02/17/2011] [Indexed: 11/30/2022] Open
Abstract
Advanced Glycated End Products (AGEs) are formed by non-enzymatic protein glycation and are implicated in several physiological aspects including cell aging and diseases. Recent data indicate that bacteria – although short lived – produce, metabolize and accumulate AGEs. Here we show that Escherichia coli cells secret AGEs by the energy-dependent efflux pump systems. Moreover, we show that in the presence of these AGEs there is an upshift of pro-inflammatory cytokins by mammalian cells. Thus, we propose that secretion of AGEs by bacteria is a novel avenue of bacterial-induced inflammation which is potentially important in the pathophysiology of bacterial infections. Moreover, the sensing of AGEs by the host cells may constitute a warning system for the presence of bacteria.
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Genetic control of amadori product degradation in Bacillus subtilis via regulation of frlBONMD expression by FrlR. Appl Environ Microbiol 2011; 77:2839-46. [PMID: 21398478 DOI: 10.1128/aem.02515-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis is capable of degrading fructosamines. The phosphorylation and the cleavage of the resulting fructosamine 6-phosphates is catalyzed by the frlD and frlB gene products, respectively. This study addresses the physiological importance of the frlBONMD genes (formerly yurPONML), revealing the necessity of their expression for growth on fructosamines and focusing on the complex regulation of the corresponding transcription unit. In addition to the known regulation by the global transcriptional regulator CodY, the frl genes are repressed by the convergently transcribed FrlR (formerly YurK). The latter causes repression during growth on substrates other than fructosamines. Additionally, we identified in the first intergenic region of the operon an FrlR binding site which is centrally located within a 38-bp perfect palindromic sequence. There is genetic evidence that this sequence, in combination with FrlR, contributes to the remarkable decrease in the transcription downstream of the first gene of the frl operon.
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Enzymatic deglycation of Amadori products in bacteria: mechanisms, occurrence and physiological functions. Appl Microbiol Biotechnol 2011; 90:399-406. [DOI: 10.1007/s00253-010-3083-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 12/21/2010] [Accepted: 12/21/2010] [Indexed: 11/25/2022]
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