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Abstract
The origin of mitochondria was a crucial event in eukaryote evolution. A recent report claimed to provide evidence, based on branch length variation in phylogenetic trees, that the mitochondrion came late in eukaryotic evolution. Here, we reinvestigate their claim with a reanalysis of the published data. We show that the analyses underpinning a late mitochondrial origin suffer from multiple fatal flaws founded in inappropriate statistical methods and analyses, in addition to erroneous interpretations.
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Affiliation(s)
- William F. Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
- Corresponding author: E-mail:
| | - Mayo Roettger
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Sriram G. Garg
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Computational Biology & Bioinformatics Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, India
| | - Giddy Landan
- Institute of Microbiology, Christian-Albrechts-University of Kiel, Germany
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2
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Barth C, Weiss MC, Roettger M, Martin WF, Unden G. Origin and phylogenetic relationships of [4Fe-4S]-containing O 2 sensors of bacteria. Environ Microbiol 2018; 20:4567-4586. [PMID: 30225854 DOI: 10.1111/1462-2920.14411] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/28/2022]
Abstract
The advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe-4S]2+ to [2Fe-2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc , FNRBs , NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe-4S] and [2Fe-2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.
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Affiliation(s)
- C Barth
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - M C Weiss
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - M Roettger
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - W F Martin
- Institute for Molecular Evolution, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
| | - G Unden
- Microbiology and Wine Research, Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Mainz, Germany
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3
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de Vries J, Fischer AM, Roettger M, Rommel S, Schluepmann H, Bräutigam A, Carlsbecker A, Gould SB. Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots. New Phytol 2016; 209:705-20. [PMID: 26358624 PMCID: PMC5049668 DOI: 10.1111/nph.13630] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/04/2015] [Indexed: 05/10/2023]
Abstract
The phytohormones cytokinin and auxin orchestrate the root meristem development in angiosperms by determining embryonic bipolarity. Ferns, having the most basal euphyllophyte root, form neither bipolar embryos nor permanent embryonic primary roots but rather an adventitious root system. This raises the questions of how auxin and cytokinin govern fern root system architecture and whether this can tell us something about the origin of that root. Using Azolla filiculoides, we characterized the influence of IAA and zeatin on adventitious fern root meristems and vasculature by Nomarski microscopy. Simultaneously, RNAseq analyses, yielding 36,091 contigs, were used to uncover how the phytohormones affect root tip gene expression. We show that auxin restricts Azolla root meristem development, while cytokinin promotes it; it is the opposite effect of what is observed in Arabidopsis. Global gene expression profiling uncovered 145 genes significantly regulated by cytokinin or auxin, including cell wall modulators, cell division regulators and lateral root formation coordinators. Our data illuminate both evolution and development of fern roots. Promotion of meristem size through cytokinin supports the idea that root meristems of euphyllophytes evolved from shoot meristems. The foundation of these roots was laid in a postembryonically branching shoot system.
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Affiliation(s)
- Jan de Vries
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Angela Melanie Fischer
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Mayo Roettger
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Sophie Rommel
- Population GeneticsHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Henriette Schluepmann
- Molecular Plant PhysiologyUtrecht UniversityPadualaan 83584CH Utrechtthe Netherlands
| | - Andrea Bräutigam
- Plant BiochemistryHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological BotanyUppsala BioCenterLinnean Centre for Plant BiologyUppsala UniversityUlls väg 24ESE‐756 51UppsalaSweden
| | - Sven Bernhard Gould
- Molecular EvolutionHeinrich‐Heine‐University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
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4
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Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 2015; 524:427-32. [PMID: 26287458 DOI: 10.1038/nature14963] [Citation(s) in RCA: 188] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/20/2015] [Indexed: 01/11/2023]
Abstract
Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.
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Affiliation(s)
- Chuan Ku
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Shijulal Nelson-Sathi
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Mayo Roettger
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Filipa L Sousa
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Peter J Lockhart
- Institute of Fundamental Sciences, Massey University, Palmerston North 4474, New Zealand
| | - David Bryant
- Department of Mathematics and Statistics, University of Otago, Dunedin 9054, New Zealand
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana 43107, Israel
| | - James O McInerney
- Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland.,Michael Smith Building, The University of Manchester, Oxford Rd, Manchester M13 9PL, UK
| | - Giddy Landan
- Genomic Microbiology Group, Institute of Microbiology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, 40225 Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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5
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Kamdar P, Kamdar F, Roettger M, Eckman P. Dental Care in Left Ventricular Assist Devices (LVAD) Patients: A Survey of Dentists. J Heart Lung Transplant 2015. [DOI: 10.1016/j.healun.2015.01.605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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6
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Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin WF. Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol 2013; 5:31-44. [PMID: 23221676 PMCID: PMC3595030 DOI: 10.1093/gbe/evs117] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2012] [Indexed: 01/12/2023] Open
Abstract
Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.
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Affiliation(s)
- Tal Dagan
- Institute of Genomic Microbiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
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7
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Abstract
Eukaryotes arose from prokaryotes, hence the root in the tree of life resides among the prokaryotic domains. The position of the root is still debated, although pinpointing it would aid our understanding of the early evolution of life. Because prokaryote evolution was long viewed as a tree-like process of lineage bifurcations, efforts to identify the most ancient microbial lineage split have traditionally focused on positioning a root on a phylogenetic tree constructed from one or several genes. Such studies have delivered widely conflicting results on the position of the root, this being mainly due to methodological problems inherent to deep gene phylogeny and the workings of lateral gene transfer among prokaryotes over evolutionary time. Here, we report the position of the root determined with whole genome data using network-based procedures that take into account both gene presence or absence and the level of sequence similarity among all individual gene families that are shared across genomes. On the basis of 562,321 protein-coding gene families distributed across 191 genomes, we find that the deepest divide in the prokaryotic world is interdomain, that is, separating the archaebacteria from the eubacteria. This result resonates with some older views but conflicts with the results of most studies over the last decade that have addressed the issue. In particular, several studies have suggested that the molecular distinctness of archaebacteria is not evidence for their antiquity relative to eubacteria but instead stems from some kind of inherently elevated rate of archaebacterial sequence change. Here, we specifically test for such a rate elevation across all prokaryotic lineages through the analysis of all possible quartets among eight genes duplicated in all prokaryotes, hence the last common ancestor thereof. The results show that neither the archaebacteria as a group nor the eubacteria as a group harbor evidence for elevated evolutionary rates in the sampled genes, either in the recent evolutionary past or in their common ancestor. The interdomain prokaryotic position of the root is thus not attributable to lineage-specific rate variation.
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Affiliation(s)
- Tal Dagan
- Institute of Botany III, Heinrich-Heine University of Düsseldorf, Düsseldorf, Germany.
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Roettger M, Martin W, Dagan T. A machine-learning approach reveals that alignment properties alone can accurately predict inference of lateral gene transfer from discordant phylogenies. Mol Biol Evol 2009; 26:1931-9. [PMID: 19443855 DOI: 10.1093/molbev/msp105] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Among the methods currently used in phylogenomic practice to detect the presence of lateral gene transfer (LGT), one of the most frequently employed is the comparison of gene tree topologies for different genes. In cases where the phylogenies for different genes are incompatible, or discordant, for well-supported branches there are three simple interpretations for the result: 1) gene duplications (paralogy) followed by many independent gene losses have occurred, 2) LGT has occurred, or 3) the phylogeny is well supported but for reasons unknown is nonetheless incorrect. Here, we focus on the third possibility by examining the properties of 22,437 published multiple sequence alignments, the Bayesian maximum likelihood trees for which either do or do not suggest the occurrence of LGT by the criterion of discordant branches. The alignments that produce discordant phylogenies differ significantly in several salient alignment properties from those that do not. Using a support vector machine, we were able to predict the inference of discordant tree topologies with up to 80% accuracy from alignment properties alone.
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Affiliation(s)
- Mayo Roettger
- Institut für Botanik III, Heinrich-Heine Universität Düsseldorf, Germany.
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9
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Deusch O, Landan G, Roettger M, Gruenheit N, Kowallik KV, Allen JF, Martin W, Dagan T. Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor. Mol Biol Evol 2008; 25:748-61. [PMID: 18222943 DOI: 10.1093/molbev/msn022] [Citation(s) in RCA: 170] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plastids are descended from a cyanobacterial symbiosis which occurred over 1.2 billion years ago. During the course of endosymbiosis, most genes were lost from the cyanobacterium's genome and many were relocated to the host nucleus through endosymbiotic gene transfer (EGT). The issue of how many genes were acquired through EGT in different plant lineages is unresolved. Here, we report the genome-wide frequency of gene acquisitions from cyanobacteria in 4 photosynthetic eukaryotes--Arabidopsis, rice, Chlamydomonas, and the red alga Cyanidioschyzon--by comparison of the 83,138 proteins encoded in their genomes with 851,607 proteins encoded in 9 sequenced cyanobacterial genomes, 215 other reference prokaryotic genomes, and 13 reference eukaryotic genomes. The analyses entail 11,569 phylogenies inferred with both maximum likelihood and Neighbor-Joining approaches. Because each phylogenetic result is dependent not only upon the reconstruction method but also upon the site patterns in the underlying alignment, we investigated how the reliability of site pattern generation via alignment affects our results: if the site patterns in an alignment differ depending upon the order in which amino acids are introduced into multiple sequence alignment--N- to C-terminal versus C- to N-terminal--then the phylogenetic result is likely to be artifactual. Excluding unreliable alignments by this means, we obtain a conservative estimate, wherein about 14% of the proteins examined in each plant genome indicate a cyanobacterial origin for the corresponding nuclear gene, with higher proportions (17-25%) observed among the more reliable alignments. The identification of cyanobacterial genes in plant genomes affords access to an important question: from which type of cyanobacterium did the ancestor of plastids arise? Among the 9 cyanobacterial genomes sampled, Nostoc sp. PCC7120 and Anabaena variabilis ATCC29143 were found to harbor collections of genes which are-in terms of presence/absence and sequence similarity-more like those possessed by the plastid ancestor than those of the other 7 cyanobacterial genomes sampled here. This suggests that the ancestor of plastids might have been an organism more similar to filamentous, heterocyst-forming (nitrogen-fixing) representatives of section IV recognized in Stanier's cyanobacterial classification. Members of section IV are very common partners in contemporary symbiotic associations involving endosymbiotic cyanobacteria, which generally provide nitrogen to their host, consistent with suggestions that fixed nitrogen supplied by the endosymbiont might have played an important role during the origin of plastids.
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Affiliation(s)
- Oliver Deusch
- Institut für Botanik III, Heinrich-Heine Universität Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany
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Abstract
Making multiple sequence alignments is one of the more commonplace procedures in modern biology. Multiple alignments are typically generated by feeding sequences into the alignment program from the N-terminus to the C-terminus. Recent results show that if the same sequences are processed from the C- to the N-terminus, a different alignment is often obtained. Because phylogenetic trees are built from alignments, the resulting trees can also differ. The new findings highlight sequence alignment as a crucial step in molecular evolutionary studies and provide straightforward measures to assess alignment reliability.
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Affiliation(s)
- William Martin
- Institute of Botany III, University of Düsseldorf, Düsseldorf, Germany.
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Abstract
OBJECTIVES This study determined the incidence of orofacial injuries in athletes attending seven neighboring Minnesota high schools who participated in varsity soccer, wrestling, and basketball during the 1996-97 academic year. METHODS Incidence was determined through athletes' written surveys and athletic trainer records. RESULTS Survey response rates ranged from 86.3 percent to 94.0 percent among schools for all sports. The incidence rate of at least one orofacial injury per athlete in a season was 27.6 percent (SD = 20.2) in soccer, 72.3 percent (SD = 9.3) in wrestling, and 55.4 percent (SD = 23.9) in basketball. Ten percent of athletes sustained dental injuries. Fixed orthodontic appliances posed a higher risk for sustaining an injury in all sports. The games-to-practices ratios for injuries were 6.8 (soccer), 1.2 (wrestling), and 1.8 (basketball). Half of the athletes believed mouthguards prevent injuries; however, only 6 percent of the athletes reported mouthguard use. Athletic trainers reported eight orofacial injuries. CONCLUSIONS The substantial rate of orofacial injuries among high school athletes participating in soccer, wrestling, and basketball needs to be minimized. Dentists should ask their adolescent patients routinely about sports participation. Policies should be developed to require school officials to report orofacial injuries, to inform athletes of their risk for orofacial injuries, and to consider mandated mouthguard use for these athletes.
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Affiliation(s)
- B Kvittem
- Ridgeview Medical Office Building, Burnsville, MN 55337, USA.
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Cooney DA, Karlowicz MG, Cubillan J, Roettger M, Jayaram HN. An enzymatic technique for measuring N-phosphonacetyl-L-aspartic acid in tissues. Cancer Treat Rep 1978; 62:1503-7. [PMID: 361225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An enzymatic technique is presented for measuring N-phosphonacetyl-L-aspartic acid (PALA; NSC-224131) in biologic specimens. Tightly bound PALA is quantitatively detached from its target enzyme, L-aspartic acid transcarbamylase (ATCase), by heating at 95 degrees C for 5 minutes. Denatured proteins are removed by centrifugation. PALA in the supernatant fluid is quantitated by exposing intact splenic ATCase to representative aliquots or subdilutions of the resultant supernatant in the presence of L-[4-14C]aspartic acid and carbamyl phosphate. After 30 minutes' incubation at 37 degrees C, unreacted L-[4-14 C]aspartic acid is dissipated enzymatically and newly formed [4-14C]carbamyl-L-aspartic acid is quantitated by scintillation spectrometry. The percentage inhibition of ATCase responds in a linear way to the logarithm of the concentration of PALA between 0.10 and 1.00 micrometer. The PALA concentration of an unknown is determined indirectly by matching the percentage inhibition caused by the unknown to the inhibition caused by a known series of standard concentrations of PALA over the linear range. This assay is sensitive, adequately reproducible despite the use of an unpurified enzyme, and notably facile. It can be used to measure PALA in plasma, urine, tissues, and tumors of subjects treated with this new oncolytic drug.
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