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Qian L, Ouyang H, Gordils-Valentin L, Hong J, Jayaraman A, Zhu X. Identification of Gut Bacterial Enzymes for Keto-Reductive Metabolism of Xenobiotics. ACS Chem Biol 2022; 17:1665-1671. [PMID: 35687750 DOI: 10.1021/acschembio.2c00312] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human gastrointestinal microbiota are known for the keto-reductive metabolism of small-molecule pharmaceuticals; however, the responsible enzymes remain poorly understood. Through in vitro biochemical assays, we report the identification of enzymes encoded in the genome of Clostridium bolteae that can reduce the ketone groups of nabumetone, hydrocortisone, and tacrolimus. The homologues to a newly identified enzyme (i.e., DesE) are potentially widely distributed in the gut microbiome. The selected enzymes display different levels of activities against additional chemicals such as two dietary compounds (i.e., raspberry ketone and zingerone), chemotherapeutic drug doxorubicin, and its aglycone metabolite doxorubicinone. Thus, our results expand the repertoire of enzymes that can reduce the ketone groups in small molecules and could serve as the basis for future personalized medicine approaches.
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Affiliation(s)
- Liangyu Qian
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Huanrong Ouyang
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Lois Gordils-Valentin
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.,Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
| | - Joshua Hong
- Department of Biology, Texas A&M University, College Station, Texas 77843, United States
| | - Arul Jayaraman
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.,Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
| | - Xuejun Zhu
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States.,Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843, United States
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Khomenkov VG, Shevelev AB, Zhukov VG, Zagustina NA, Bezborodov AM, Popov VO. Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic degradation in microorganisms: A review. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683808020014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Brandão PFB, Clapp JP, Bull AT. Diversity of nitrile hydratase and amidase enzyme genes in Rhodococcus erythropolis recovered from geographically distinct habitats. Appl Environ Microbiol 2003; 69:5754-66. [PMID: 14532022 PMCID: PMC201182 DOI: 10.1128/aem.69.10.5754-5766.2003] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2003] [Accepted: 07/09/2003] [Indexed: 11/20/2022] Open
Abstract
A molecular screening approach was developed in order to amplify the genomic region that codes for the alpha- and beta-subunits of the nitrile hydratase (NHase) enzyme in rhodococci. Specific PCR primers were designed for the NHase genes from a collection of nitrile-degrading actinomycetes, but amplification was successful only with strains identified as Rhodococcus erythropolis. A hydratase PCR product was also obtained from R. erythropolis DSM 43066(T), which did not grow on nitriles. Southern hybridization of other members of the nitrile-degrading bacterial collection resulted in no positive signals other than those for the R. erythropolis strains used as positive controls. PCR-restriction fragment length polymorphism-single-strand conformational polymorphism (PRS) analysis of the hydratases in the R. erythropolis strains revealed unique patterns that mostly correlated with distinct geographical sites of origin. Representative NHases were sequenced, and they exhibited more than 92.4% similarity to previously described NHases. The phylogenetic analysis and deduced amino acid sequences suggested that the novel R. erythropolis enzymes belonged to the iron-type NHase family. Some different residues in the translated sequences were located near the residues involved in the stabilization of the NHase active site, suggesting that the substitutions could be responsible for the different enzyme activities and substrate specificities observed previously in this group of actinomycetes. A similar molecular screening analysis of the amidase gene was performed, and a correlation between the PRS patterns and the geographical origins identical to the correlation found for the NHase gene was obtained, suggesting that there was coevolution of the two enzymes in R. erythropolis. Our findings indicate that the NHase and amidase genes present in geographically distinct R. erythropolis strains are not globally mixed.
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Affiliation(s)
- Pedro F B Brandão
- Research School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
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Innes D, Beacham IR, Beven CA, Douglas M, Laird MW, Joly JC, Burns DM. The cryptic ushA gene (ushA(c)) in natural isolates of Salmonella enterica (serotype Typhimurium) has been inactivated by a single missense mutation. MICROBIOLOGY (READING, ENGLAND) 2001; 147:1887-1896. [PMID: 11429465 DOI: 10.1099/00221287-147-7-1887] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two mutational mechanisms, both supported by experimental studies, have been proposed for the evolution of new or improved enzyme specificities in bacteria. One mechanism involves point mutation(s) in a gene conferring novel substrate specificity with partial or complete loss of the original (wild-type) activity of the encoded product. The second mechanism involves gene duplication followed by silencing (inactivation) of one of these duplicates. Some of these 'silent genes' may still be transcribed and translated but produce greatly reduced levels of functional protein; gene silencing, in this context, is distinct from the more common associations with bacterial partitioning sequences, and with genes which are no longer transcribed or translated. Whereas most Salmonella enterica strains are ushA(+), encoding an active 5'-nucleotidase (UDP-sugar hydrolase), some natural isolates, including most genetically related strains of serotype Typhimurium, have an ushA allele (designated ushA(c)) which produces a protein with, comparatively, very low 5'-nucleotidase activity. Previous sequence analysis of cloned ushA(c) and ushA(+) genes from serotype Typhimurium strain LT2 and Escherichia coli, respectively, did not reveal any changes which might account for the significantly different 5'-nucleotidase activities. The mechanism responsible for this reduced activity of UshA(c) has hitherto not been known. Sequence analysis of Salmonella ushA(+) and ushA(c) alleles indicated that the relative inactivity of UshA(c) may be due to one, or more, of four amino acid substitutions. One of these changes (S139Y) is in a sequence motif that is conserved in 5'-nucleotidases across a range of diverse prokaryotic and eukaryotic species. Site-directed mutagenesis confirmed that a Tyr substitution of Ser-139 in Salmonella UshA(+) was solely responsible for loss of 5'-nucleotidase activity. It is concluded that the corresponding single missense mutation is the cause of the UshA(c) phenotype. This is the first reported instance of gene inactivation in natural isolates of bacteria via a missense mutation. These results support a model of evolution of new enzymes involving a 'silent gene' which produces an inactive, or relatively inactive, product, and are also consistent with the evolution of a novel, but unknown, enzyme specificity by a single amino acid change.
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Affiliation(s)
- David Innes
- School of Biomolecular and Biomedical Science, Griffith University, Brisbane, Qld 4111, Australia1
| | - Ifor R Beacham
- School of Health Science, Griffith University, PMB 50 Gold Coast Mail Centre, Gold Coast, Qld 4217, Australia2
| | - Carie-Anne Beven
- School of Health Science, Griffith University, PMB 50 Gold Coast Mail Centre, Gold Coast, Qld 4217, Australia2
| | - Meaghan Douglas
- School of Biomolecular and Biomedical Science, Griffith University, Brisbane, Qld 4111, Australia1
| | - Michael W Laird
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA3
| | - John C Joly
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA3
| | - Dennis M Burns
- School of Biomolecular and Biomedical Science, Griffith University, Brisbane, Qld 4111, Australia1
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Beven CA, Dieckelmann M, Beacham IR. A strain of Pseudomonas fluorescens with two lipase-encoding genes, one of which possibly encodes cytoplasmic lipolytic activity. J Appl Microbiol 2001; 90:979-87. [PMID: 11412328 DOI: 10.1046/j.1365-2672.2001.01333.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS A lipase-encoding gene (lipA) from a psychrotrophic strain of Pseudomonas fluorescens C9 has previously been characterized. It was also shown that when this gene was insertionally-inactivated, lipase activity was retained, suggesting that a second lipase may be present in this strain. The aim of this study was to determine whether this was the case. METHODS AND RESULTS Using molecular cloning, chromosomal mutagenesis and enzymatic analysis, the presence of a second lipase-encoding gene (lipB) has been confirmed. The molecular weights of the putative products of lipA and lipB are 33 and 64.5 kDa, respectively, and their sequences are quite dissimilar (< 10% sequence identity). The lipB gene encodes a secreted lipase and is solely responsible for the 'lipolytic phenotype' of Ps. fluorescens C9. Expression of the lipA gene can be detected when expressed using an expression vector, but activity was only detected intracellularly in Ps. fluorescens C9, and not in the culture medium. CONCLUSION Pseudomonas fluorescens C9 contains two dissimilar lipases. One (LipB) is secreted and responsible for the lipolytic phenotype; the evidence suggests that the other (LipA) could be intracellular, but it could be secreted and not detectable. SIGNIFICANCE AND IMPACT OF THE STUDY Bacteria may contain more than one lipase activity. Ascribing phenotypes to particular enzymes therefore requires mutational analysis. The notion of an intracellular lipase activity is novel, and, if further substantiated, begs the question as to its normal substrate and physiological role.
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Affiliation(s)
- C A Beven
- School of Health Science, Griffith University, Gold Coast, Queensland, Australia
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Burns DM, Burger MJ, Beacham IR. Silent genes in bacteria: the previously designated 'cryptic' ilvHI locus of 'Salmonella typhimurium LT2' is active in natural isolates. FEMS Microbiol Lett 1995; 131:167-72. [PMID: 7557326 DOI: 10.1111/j.1574-6968.1995.tb07772.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gene ilvG in Escherichia coli K-12 and ilvI in 'Salmonella typhimurium LT2' (S. enterica serotype Typhimurium, strain LT2) are inactive due to frameshift or nonsense mutations, respectively. These inactive genes have been suggested to be part of 'cryptic' genetic systems which are defined as being of long-term regulatory and evolutionary significance. We have shown that the nonsense mutation in ilvI is present only in derivatives of the laboratory strain 'S. typhimurium LT2'. All natural isolates of Salmonella examined have an arginine codon at the corresponding location of their ilvI sequences. Further, two randomly selected natural isolates of serotype Typhimurium are shown to each have an active ALS III isozyme. Our findings strongly suggest that the only Salmonella strains which lack a functional ilvHI locus are LT2 isolates. We suggest that the mutations leading to inactivation of both ilvI in 'S. typhimurium LT2' and ilvG in E. coli K-12 are more likely to have been acquired during laboratory storage and/or cultivation, rather than representing cryptic systems of gene regulation.
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Affiliation(s)
- D M Burns
- Faculty of Science and Technology, Griffith University, Nathan, Brisbane, Qld, Australia
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van der Meer JR, de Vos WM, Harayama S, Zehnder AJ. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev 1992; 56:677-94. [PMID: 1480115 PMCID: PMC372894 DOI: 10.1128/mr.56.4.677-694.1992] [Citation(s) in RCA: 226] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Microorganisms in the environment can often adapt to use xenobiotic chemicals as novel growth and energy substrates. Specialized enzyme systems and metabolic pathways for the degradation of man-made compounds such as chlorobiphenyls and chlorobenzenes have been found in microorganisms isolated from geographically separated areas of the world. The genetic characterization of an increasing number of aerobic pathways for degradation of (substituted) aromatic compounds in different bacteria has made it possible to compare the similarities in genetic organization and in sequence which exist between genes and proteins of these specialized catabolic routes and more common pathways. These data suggest that discrete modules containing clusters of genes have been combined in different ways in the various catabolic pathways. Sequence information further suggests divergence of catabolic genes coding for specialized enzymes in the degradation of xenobiotic chemicals. An important question will be to find whether these specialized enzymes evolved from more common isozymes only after the introduction of xenobiotic chemicals into the environment. Evidence is presented that a range of genetic mechanisms, such as gene transfer, mutational drift, and genetic recombination and transposition, can accelerate the evolution of catabolic pathways in bacteria. However, there is virtually no information concerning the rates at which these mechanisms are operating in bacteria living in nature and the response of such rates to the presence of potential (xenobiotic) substrates. Quantitative data on the genetic processes in the natural environment and on the effect of environmental parameters on the rate of evolution are needed.
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Affiliation(s)
- J R van der Meer
- Department of Microbiology, Wageningen Agricultural University, The Netherlands
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Kobayashi H, Viale AM, Takabe T, Akazawa T, Wada K, Shinozaki K, Kobayashi K, Sugiura M. Sequence and expression of genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase from Chromatium vinosum. Gene 1991; 97:55-62. [PMID: 1899846 DOI: 10.1016/0378-1119(91)90009-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A DNA fragment bearing genes for the large (rbcL) and small (rbcS) subunits of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) was cloned from the photosynthetic purple sulfur bacterium Chromatium vinosum. Enzymatically fully active RuBisCO was synthesized in Escherichia coli cells when the cloned DNA was placed downstream of tac promoter. Nucleotide (nt) sequences of rbcL-rbcS were more homologous to cyanobacterial counterparts than to those from Alcaligenes eutrophus or higher plants. However, the amino acid (aa) sequence in a domain responsible for CO2 activation in the C. vinosum rbcL product resembled the corresponding aa sequence in higher plant RuBisCos, but not in the cyanobacterial enzymes. Chemically determined aa sequences at the N terminals of both subunits of RuBisCO purified from C. vinosum were not identical to those deduced from the nt sequences, although they were completely the same as aa sequences deduced from rbcA-rbcB, another locus encoding RuBisCO in C. vinosum. Therefore, the rbcL-rbcS locus seems to be barely expressed under a standard condition for photoautotrophic growth. The homology of the nt sequences between rbcL and rbcA was 82%, and that between rbcS and rbcB was 63%, whereas the codon usages of these genes were basically identical. The rbcL-rbcS and rbcA-rbcB loci therefore must have evolved from a common ancestral set of genes after duplication, instead of lateral gene transfer.
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Affiliation(s)
- H Kobayashi
- Radioisotope Research Center, Nagoya University, Japan
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Distinct properties of Escherichia coli products of plant-type ribulose-1,5-bisphosphate carboxylase/oxygenase directed by two sets of genes from the photosynthetic bacterium Chromatium vinosum. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)44764-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Houmard J, Capuano V, Coursin T, Tandeau de Marsac N. Genes encoding core components of the phycobilisome in the cyanobacterium Calothrix sp. strain PCC 7601: occurrence of a multigene family. J Bacteriol 1988; 170:5512-21. [PMID: 2461358 PMCID: PMC211645 DOI: 10.1128/jb.170.12.5512-5521.1988] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The phycobilisome is the major light-harvesting complex of cyanobacteria. It is composed of a central core from which six rods radiate. Allphycocyanin, an alpha beta oligomer (alpha AP and beta AP), is the main component of the core which also contains three other phycobiliproteins (alpha APB, beta 18.3, and L92CM) and a small linker polypeptide (L7.8C). By heterologous DNA hybridization, two EcoRI DNA fragments of 3.5 and 3.7 kilobases have been cloned from the chromatically adapting cyanobacterium Calothrix sp. strain PCC 7601. Nucleotide sequence determination has allowed the identification of five apc genes: apcA1 (alpha AP1), apcA2 (alpha AP2), apcB1 (beta AP1), apcC (L7.8C), and apcE (L92CM). Four of these genes are adjacent on the chromosome and form the apcEA1B1C gene cluster. In contrast, no genes have been found close to the apcA2 gene which is carried by the 3.5-kilobase EcoRI fragment. Transcriptional analysis and 5'-end-mapping experiments were performed. The results obtained demonstrate that the apcEA1B1C gene cluster forms an operon from which segmented transcripts originate, whereas the apcA2 gene behaves as a monocistronic unit. Qualitatively, the same transcripts were identified regardless of the light wavelengths received during cell growth. The deduced amino acid sequences of the apc gene products are very similar to their known homologs of either cyanobacterial or eucaryotic origin. It was interesting, however, that in the apcA1 and apcA2 genes, whose products correspond to alpha-type allophycocyanin subunits, nucleotide sequences were more conserved (67%) than were the deduced amino acid sequences (59%).
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Affiliation(s)
- J Houmard
- Unité de Physiologie Microbienne, Centre National de la Recherche Scientifique, Paris, France
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