Cited by 117Origins and Evolution of LifeEvolution and Genetic DynamicsGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 129 of the 135 references it cites were found in a registry or an index.

Origin and evolution of metabolic pathways

Fani, Renato, Fondi, Marco·2009·Physics of Life Reviews

DOI 10.1016/j.plrev.2008.12.003

Open this paper in CoChat — free account

Abstract

The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present in the ancestral environment, imposed an important selective pressure, favoring those primordial heterotrophic cells which became capable of synthesizing those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less-dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria and Eukarya revealed that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the arisal of new metabolic abilities. Among these gene elongations, gene and operon duplications undoubtedly played a major role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence giving rise to new genes coding for new metabolic abilities. Gene duplication has been invoked in the different schemes proposed to explain why and how the extant metabolic pathways have arisen and shaped. Both the analysis of completely sequenced genomes and directed evolution experiments strongly support one of them, i.e. the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis and nitrogen fixation, suggested that other different hypothesis, i.e. the retrograde hypothesis or the semi-enzymatic theory, may account for the arisal of some metabolic routes.

Integrity signals

Registry

Crossref · 10.1016/j.plrev.2008.12.003

Cites

129 of 129 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
The Evolutionary Fate and Consequences of Duplicate Genes
Lynch, M., & Conery, J. S. (2000) · Science · doi:10.1126/science.290.5494.1151 · Cited by 4,988
Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology
Neidhardt, F. C., & Ingraham, J. L. (1987) · Medical Entomology and Zoology · Cited by 4,089
Escherichia coli and Salmonella typhimurium: Cellular and molecular biology
Lejeune, P. (1988) · Biochimie · doi:10.1016/0300-9084(88)90119-8 · Cited by 4,086
A Production of Amino Acids Under Possible Primitive Earth Conditions
Miller, S. L. (1953) · Science · doi:10.1126/science.117.3046.528 · Cited by 3,522
Fundamentals of molecular evolution
(1991) · Journal of Human Evolution · doi:10.1016/0047-2484(91)90069-8 · Cited by 1,669
The Probability of Duplicate Gene Preservation by Subfunctionalization
Lynch, M., & Force, A. G. (2000) · Genetics · doi:10.1093/genetics/154.1.459 · Cited by 1,559
Biological Nitrogen Fixation
Burris, R. H., & Roberts, G. P. (1993) · Annual Review of Nutrition · doi:10.1146/annurev.nu.13.070193.001533 · Cited by 1,464
Evolving Genes and Proteins
Bryson, V., & Vogel, H. J. (1965) · Science · doi:10.1126/science.147.3653.68 · Cited by 1,343
ENZYME RECRUITMENT IN EVOLUTION OF NEW FUNCTION
Jensen, R. A. (1976) · Annual Review of Microbiology · doi:10.1146/annurev.mi.30.100176.002205 · Cited by 1,111
Genetic Control of Biochemical Reactions in Neurospora
Beadle, G. W., & Tatum, E. L. (1941) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.27.11.499 · Cited by 1,062
Complexes of sequential metabolic enzymes
Srere, P. A. (1987) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.56.070187.000513 · Cited by 1,058
The universal ancestor
Woese, C. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6854 · Cited by 1,053
Origin and evolution of the elements
Prantzos, N., Vangioni–Flam, E., & Cassé, M. (1993) · Cambridge University Press eBooks · Cited by 1,051
A minimal gene set for cellular life derived by comparison of complete bacterial genomes
Mushegian, A. R., & Koonin, E. V. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.19.10268 · Cited by 916
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia
Aury, J., Jaillon, O., Duret, L., Noël, B., Jubin, C., Porcel, B. M., Segurens, B., Daubin, V., Anthouard, V., Aiach, N. G., et al. (2006) · Nature · doi:10.1038/nature05230 · Cited by 872
On the evolution of cells
Woese, C. R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.132266999 · Cited by 762
Evolving Genes and Proteins
(1965) · Elsevier eBooks · doi:10.1016/c2013-0-11981-2 · Cited by 747
Oxygen relations of nitrogen fixation in cyanobacteria
Fay, P. K. (1992) · Microbiological Reviews · doi:10.1128/mr.56.2.340-373.1992 · Cited by 704
Phylogenomics: The beginning of incongruence?
JEFFROY, O., BRINKMANN, H., DELSUC, F., & PHILIPPE, H. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.02.003 · Cited by 698
Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters
Lawrence, J. G., & Roth, J. R. (1996) · Genetics · doi:10.1093/genetics/143.4.1843 · Cited by 689
Comparative genomics, minimal gene-sets and the last universal common ancestor
Koonin, E. V. (2003) · Nature Reviews Microbiology · doi:10.1038/nrmicro751 · Cited by 661
The Origin of Life.
Just, T., Oparin, A. I., & Morgulis, S. (1938) · The American Midland Naturalist · doi:10.2307/2420646 · Cited by 626
On the Evolution of Biochemical Syntheses
Horowitz, N. H. (1945) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.31.6.153 · Cited by 610
Archaea and the prokaryote-to-eukaryote transition
Brown, J. R., & Doolittle, W. F. (1997) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.61.4.456-502.1997 · Cited by 485
TANDEM GENETIC DUPLICATIONS IN PHAGE AND BACTERIA
Anderson, R. P., & Roth, J. R. (1977) · Annual Review of Microbiology · doi:10.1146/annurev.mi.31.100177.002353 · Cited by 467
How often do duplicated genes evolve new functions?
Walsh, J. B. (1995) · Genetics · doi:10.1093/genetics/139.1.421 · Cited by 418
Fundamentals of molecular evolution
Mindell, D. P. (1991) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(91)90046-z · Cited by 406
On the origin of genomes and cells within inorganic compartments
Koonin, E. V., & Martin, W. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.09.006 · Cited by 406
PSEUDOALLELISM AND GENE EVOLUTIONPreprint
Lewis, E. B. (1951) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1951.016.01.014 · Cited by 361
The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time
Lazcano, A., & Miller, S. L. (1996) · Cell · doi:10.1016/s0092-8674(00)81263-5 · Cited by 359
FRACTIONATION AND STRUCTURAL ASSESSMENT OF OLIGOSACCHARIDES AND GLYCOPEPTIDES BY USE OF IMMOBILIZED LECTINS
Osawa, T., & Tsuji, T. (1987) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.56.070187.000321 · Cited by 357
Beginnings of biospheric evolution and their biogeochemical consequences
Cloud, P. (1976) · Paleobiology · doi:10.1017/s009483730000498x · Cited by 333
The fundamentals of nitrogen fixation
Postgate, J. R. (1978) · Medical Entomology and Zoology · Cited by 320
Histidine biosynthetic pathway and genes: structure, regulation, and evolution
Alifano, P., Fani, R., Lió, P., Lazcano, A., Bazzicalupo, M., Carlomagno, M. S., & Bruni, C. B. (1996) · Microbiological Reviews · doi:10.1128/mr.60.1.44-69.1996 · Cited by 300
The terpenoid theory of the origin of cellular life: the evolution of terpenoids to cholesterol
Ourisson, G., & Nakatani, Y. (1994) · Chemistry & Biology · doi:10.1016/1074-5521(94)90036-1 · Cited by 289
The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?
Koonin, E. V. (2006) · Biology Direct · doi:10.1186/1745-6150-1-22 · Cited by 289
Understanding Enzyme Superfamilies
Babbitt, P. C., & Gerlt, J. A. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.49.30591 · Cited by 273
Gene transfer, speciation, and the evolution of bacterial genomes
Lawrence, J. G. (1999) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(99)00010-7 · Cited by 245
Comparable Rates of Gene Loss and Functional Divergence After Genome Duplications Early in Vertebrate Evolution
Nadeau, J. H., & Sankoff, D. (1997) · Genetics · doi:10.1093/genetics/147.3.1259 · Cited by 234
On earlier states of the biochemical system
Yčas, M. (1974) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(74)80035-4 · Cited by 228
Increased glycolytic flux as an outcome of whole-genome duplication in yeast
Conant, G. C., & Wolfe, K. H. (2007) · Molecular Systems Biology · doi:10.1038/msb4100170 · Cited by 222
Homology among (βα) 8 barrels: implications for the evolution of metabolic pathways 1 1Edited by G. Von Heijne
Copley, R. R., & Peer Bork, B. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4152 · Cited by 209
Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach
Copley, S. D. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01562-0 · Cited by 191
RATE OF GENE SILENCING AT DUPLICATE LOCI: A THEORETICAL STUDY AND INTERPRETATION OF DATA FROM TETRAPLOID FISHES
Li, W. (1980) · Genetics · doi:10.1093/genetics/95.1.237 · Cited by 189
Gene duplication and biased functional retention of paralogs in bacterial genomes
Gevers, D., Vandepoele, K., Simillion, C., & de Peer, Y. V. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.02.007 · Cited by 186
Molecular Evolution of Nitrogen Fixation: The Evolutionary History of the nifD, nifK, nifE, and nifN Genes
Fani, R., Gallo, R., & Lió, P. (2000) · Journal of Molecular Evolution · doi:10.1007/s002390010061 · Cited by 185
Evolution in biosynthetic pathways: two enzymes catalyzing consecutive steps in methionine biosynthesis originate from a common ancestor and possess a similar regulatory region.
Belfaiza, J., Parsot, C., Martel, A., de la Tour, C. B., Margarita, D., Cohen, G. N., & Saint‐Girons, I. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.4.867 · Cited by 184
The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution
Meléndez‐Hevia, E., Waddell, T. G., & Cascante, M. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02338838 · Cited by 180
The fundamentals of nitrogen fixation
Eisbrenner, G. (1983) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(83)90119-6 · Cited by 174
Directed evolution of a (βα) 8 -barrel enzyme to catalyze related reactions in two different metabolic pathways
Jürgens, C., Strom, A. M., Wegener, D., Hettwer, S., Wilmanns, M., & Sterner, R. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.160255397 · Cited by 170
SPECULATIONS ON THE ORIGINS AND EVOLUTION OF PHOTOSYNTHESIS
Granick, S. (1957) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.1957.tb49665.x · Cited by 156
Structural conservation in parallel .beta./.alpha.-barrel enzymes that catalyze three sequential reactions in the pathway of tryptophan biosynthesis
Wilmanns, M., Hyde, C. C., Davies, D. R., Kirschner, K., & Jansonius, J. N. (1991) · Biochemistry · doi:10.1021/bi00102a006 · Cited by 155
Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons
Carlomagno, M. S., Chiariotti, L., Alifano, P., Nappo, A. G., & Bruni, C. B. (1988) · Journal of Molecular Biology · doi:10.1016/0022-2836(88)90194-5 · Cited by 151
The Evolution of Metabolic Function
Mortlock, R. P. (1992) · Cited by 146
A minimal estimate for the gene content of the last universal common ancestor—exobiology from a terrestrial perspective
Ouzounis, C., Kunin, V., Darzentas, N., & Goldovsky, L. (2005) · Research in Microbiology · doi:10.1016/j.resmic.2005.06.015 · Cited by 146
A community experiment with fully open and published peer review.
Koonin, E., Landweber, L. F., & Lipman, D. J. (2006) · Biology Direct · doi:10.1186/1745-6150-1-1 · Cited by 145
Evolution of gene families
Ohta, T. (2000) · Gene · doi:10.1016/s0378-1119(00)00428-5 · Cited by 141
The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase.
Nyunoya, H., & Lusty, C. J. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.15.4629 · Cited by 141
The Evolution of Bacterial Enzyme Systems
Hegeman, G. D., & Rosenberg, S. L. (1970) · Annual Review of Microbiology · doi:10.1146/annurev.mi.24.100170.002241 · Cited by 140
Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change
Xie, G. G., Keyhani, N. O., Bonner, C. A., & Jensen, R. A. (2003) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.67.3.303-342.2003 · Cited by 138
Divergence of the Hyperthermophilic Archaea Pyrococcus furiosus and P. horikoshii Inferred From Complete Genomic Sequences
Maeder, D. L., Weiss, R. B., Dunn, D. M., Cherry, J. L., Grau, J. M. G., DiRuggiero, J., & Robb, F. T. (1999) · Genetics · doi:10.1093/genetics/152.4.1299 · Cited by 136
How long did it take for life to begin and evolve to cyanobacteria?
Lazcano, A., & Miller, S. L. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160399 · Cited by 135
Evolution in the Microbial World
Savile, D. B. O., Carlile, M., & Skehel, J. J. (1975) · Mycologia · doi:10.2307/3758249 · Cited by 129
Cloning of the HSP70 gene from Halobacterium marismortui: relatedness of archaebacterial HSP70 to its eubacterial homologs and a model for the evolution of the HSP70 gene
Gupta, R. S., & Singh, B. (1992) · Journal of Bacteriology · doi:10.1128/jb.174.14.4594-4605.1992 · Cited by 127
Phylogeny of nitrogenase sequences inFrankia and other nitrogen-fixing microorganisms
Normand, P., & Bouquet, J. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02602914 · Cited by 124
The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution
Meléndez‐Hevia, E., Waddell, T. G., & Cascante, M. (1996) · Journal of Molecular Evolution · doi:10.1007/pl00006089 · Cited by 124
Evolution of gene fusions: horizontal transfer versus independent events
Yanai, I., Wolf, Y. I., & Koonin, E. V. (2002) · Genome biology · doi:10.1186/gb-2002-3-5-research0024 · Cited by 116
Promoter-creating mutations in Pseudomonas putida: a model system for the study of mutation in starving bacteria.
Kasak, L., Hõrak, R., & Kivisaar, M. (1997) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.94.7.3134 · Cited by 113
The Origin of Life.
Pierpoint, W. S., & Bernal, J. D. (1967) · Man · doi:10.2307/2799350 · Cited by 113
[147] Enzymes and intermediates of histidine biosynthesis in Salmonella typhimurium
Martin, R. G., Berberich, M. A., Ames, B. N., Davis, W. W., Goldberger, R. F., & Yourno, J. (1971) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(71)17003-6 · Cited by 110
Structure and mechanism of a sub-family of enzymes related to N -acetylneuraminate lyase 1 1Edited by F. E. Cohen
Lawrence, M. C., Barbosa, J. A. R. G., Smith, B. J., Hall, N. E., Pilling, P. A., Ooi, H. C., & Marcuccio, S. M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0769 · Cited by 109
Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
Price, M. N., Dehal, P., & Arkin, A. P. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030175 · Cited by 105
Evolution of biosynthetic pathways: a common ancestor for threonine synthase, threonine dehydratase and D‐serine dehydratase.
Parsot, C. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04600.x · Cited by 104
The Origin and Evolution of The Cell
(1993) · doi:10.1142/1909 · Cited by 101
The Evolution of Biochemical Syntheses — Retrospect and Prospect
Horowitz, N. H. (1965) · Elsevier eBooks · doi:10.1016/b978-1-4832-2734-4.50009-7 · Cited by 100
Evolution of Heme and Chlorophyll
Granick, S. (1965) · Elsevier eBooks · doi:10.1016/b978-1-4832-2734-4.50014-0 · Cited by 100
Efflux pump genes of the resistance-nodulation-division family in Burkholderia cenocepacia genome
Guglierame, P., Pasca, M. R., Rossi, E. D., Buroni, S., Arrigo, P., Manina, G., & Riccardi, G. (2006) · BMC Microbiology · doi:10.1186/1471-2180-6-66 · Cited by 100
The cell-bag of enzymes or network of channels?
Mathews, C. K. (1993) · Journal of Bacteriology · doi:10.1128/jb.175.20.6377-6381.1993 · Cited by 98
Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis
Gerlt, J. A., & Babbitt, P. C. (1998) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(98)80091-4 · Cited by 93
Biosynthesis of Histidine
Winkler, M. E., & Ramos‐Montañez, S. (2009) · EcoSal Plus · doi:10.1128/ecosalplus.3.6.1.9 · Cited by 90
Glycyl radical enzymes: a conservative structural basis for radicals
Eklund, H., & Fontecave, M. (1999) · Structure · doi:10.1016/s0969-2126(00)80019-2 · Cited by 89
The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case
Fani, R., Brilli, M., Fondi, M., & Lió, P. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s2-s4 · Cited by 88
Evolution of microbial life
Dijkhuizen, L. (1996) · Cited by 85
Multiple copies of ammonia monooxygenase (amo) operons have evolved under biased AT/GC mutational pressure in ammonia-oxidizing autotrophic bacteria
Klotz, M. G., & Norton, J. M. (1998) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1998.tb13288.x · Cited by 83
The Last Common Ancestor: What's in a name?
Delaye, L., Becerra, A., & Lazcano, A. (2005) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-005-5760-3 · Cited by 83
Modular multidomain phosphoryl transfer proteins of bacteria
Reizer, J., & Saier, M. H. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80059-0 · Cited by 82
Molecular evolution of the histidine biosynthetic pathway
Fani, R., Li�, P., & Lazcano, A. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00173156 · Cited by 82
Evolution of microbial life
Roberts, D., Sharp, P. J., Alderson, G., & Collins, M. (1997) · University of Groningen research database (University of Groningen / Centre for Information Technology) · Cited by 78
Nucleotide sequence of lysC gene encoding the lysine-sensitive aspartokinase III of Escherichia coli K12. Evolutionary pathway leading to three isofunctional enzymes.
Cassan, M., Parsot, C., Cohen, G. N., & Patte, J.-C. (1986) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)36051-9 · Cited by 74
Gene duplication in the evolution of the two complementing domains of Gram-negative bacterial tetracycline efflux proteins
Rubin, R. A., Levy, S. B., Heinrikson, R. L., & Kézdy, F. J. (1990) · Gene · doi:10.1016/0378-1119(90)90489-e · Cited by 74
The evolution of the histidine biosynthetic genes in prokaryotes: A common ancestor for the hisA and hisF genes
Fani, R., Lió, P., Chiarelli, I., & Bazzicalupo, M. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178849 · Cited by 71
Experimental Models of Acquisitive Evolution
Lin, E. C. C., Hacking, A. J., & Aguilar, J. (1976) · BioScience · doi:10.2307/1297270 · Cited by 69
Catalysis of peptide bond formation by histidyl-histidine in a fluctuating clay environment
White, D. H., & Erickson, J. C. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01804979 · Cited by 64
Prebiotic synthesis of histidine
Shen, C., Yang, L., Miller, S. L., & Oro, J. A. (1990) · Journal of Molecular Evolution · doi:10.1007/bf02109492 · Cited by 62
Microbial evolution : gene establishment, survival, and exchange
Miller, R. V., & Day, M. J. (2004) · Cited by 59
The Origin and Evolution of Operons: The Piecewise Building of the Proteobacterial Histidine Operon
Fani, R., Brilli, M., & Liò, P. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0198-1 · Cited by 59
Gene Duplication and the Origin of Repetitive Protein StructuresPreprint
McLachlan, A. (1987) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1987.052.01.048 · Cited by 59
Genome increase as a clock for the origin and evolution of life.
Sharov, A. A. (2006) · Biology Direct · doi:10.1186/1745-6150-1-17 · Cited by 56
Nucleotide sequence ofthrCand of the transcription tennination region of the threonine operon inEscherichia coliK12
Parsot, C., Cossart, P., Saint‐Girons, I., & Cohen, G. N. (1983) · Nucleic Acids Research · doi:10.1093/nar/11.21.7331 · Cited by 54
The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis
Fondi, M., Brilli, M., Emiliani, G., Paffetti, D., & Fani, R. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s2-s3 · Cited by 53
Evolution of asymbiotic nitrogen fixation
Silver, W. S., & Postgate, J. R. (1973) · Journal of Theoretical Biology · doi:10.1016/0022-5193(73)90160-4 · Cited by 51
Catalysis by a prebiotic nucleotide analog of histidine
Maurel, M., & Ninio, J. (1987) · Biochimie · doi:10.1016/0300-9084(87)90094-0 · Cited by 51
Widespread protein sequence similarities: origins of Escherichia coli genes
Labedan, B., & Riley, M. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.6.1585-1588.1995 · Cited by 49
Molecular Evolution of hisB Genes
Brilli, M., & Fani, R. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2547-x · Cited by 48
Evolution of a new enzymatic function by recombination within a gene.
Hall, B. G., & Zuzel, T. (1980) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.77.6.3529 · Cited by 47
Evolutionary aspects of urea cycle enzyme genes
Takiguchi, M., Matsubasa, T., Amaya, Y., & Mori, M. (1989) · BioEssays · doi:10.1002/bies.950100506 · Cited by 44
Evolution of the Structure and Chromosomal Distribution of Histidine Biosynthetic Genes
Fani, R., Mori, E., Tamburini, E., & Lazcano, A. (1998) · Origins of Life and Evolution of Biospheres · doi:10.1023/a:1006531526299 · Cited by 37
The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor
de Rosa, R., & Labedan, B. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025843 · Cited by 36
On the levels of enzymatic substrate specificity: Implications for the early evolution of metabolic pathways
Lazcano, A., Villagómez, E. D., Mills, T., & Oro, J. A. (1995) · Advances in Space Research · doi:10.1016/s0273-1177(99)80106-9 · Cited by 30
Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes
Fani, R., Tamburini, E., Mori, E., Lazcano, A., Lió, P., Barberio, C., Casalone, E., Cavalieri, D., Perito, B., & Polsinelli, M. (1997) · Gene · doi:10.1016/s0378-1119(97)00146-7 · Cited by 27
Prebiotic synthesis of histidyl-histidine
Shen, C., Mills, T., & Oro, J. A. (1990) · Journal of Molecular Evolution · doi:10.1007/bf02109493 · Cited by 26
Gene duplications and horizontal gene transfer during early evolution
Gogarten, J. P., Hilario, E., & Olendzenski, L. (1996) · Origins of Life and Evolution of Biospheres · doi:10.1007/bf02459760 · Cited by 25
Function of hisF and hisH gene products in histidine biosynthesis.
Rieder, G., Merrick, M. J., Castorph, H., & Kleiner, D. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)36634-6 · Cited by 24
New wine from old barrels.
Gerlt, J. A. (2000) · Nature Structural Biology · doi:10.1038/73249 · Cited by 24
Transcriptional Reprogramming and Backup Between Duplicate Genes: Is It a Genomewide Phenomenon?
He, X., & Zhang, J. (2005) · Genetics · doi:10.1534/genetics.105.049890 · Cited by 24
News, opinion and letters
Ohno, S. (1972) · Developmental Biology · doi:10.1016/0012-1606(72)90117-0 · Cited by 24
The origin and evolution of eucaryal HIS7 genes: from metabolon to bifunctional proteins?
Brilli, M., & Fani, R. (2004) · Gene · doi:10.1016/j.gene.2004.06.033 · Cited by 22
Sequence similarities between tryptophan synthase β subunit and other pyridoxal-phosphate-dependent enzymes
Peer Bork, B., & Rohde, K. E. (1990) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(90)90830-g · Cited by 19
Biosynthesis of Histidine
Winkler, M. E., & Ramos‐Montañez, S. (2009) · EcoSal · doi:10.1128/ecosal.3.6.1.9 · Cited by 19
A metabolic force for gene clustering
Svetic, R. (2003) · Bulletin of Mathematical Biology · doi:10.1016/j.bulm.2003.09.008 · Cited by 17
[44] Acquisition of new metabolic activities by microbial populations
Hall, B. G., & Hauer, B. (1993) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(93)24045-v · Cited by 16
Expression of horizontally transferred gene clusters: activation by promoter-generating mutations
Dabizzi, S., Ammannato, S., & Fani, R. (2001) · Research in Microbiology · doi:10.1016/s0923-2508(01)01228-1 · Cited by 16
Gene Duplication and Gene Loading
Fani, R. (2014) · ASM Press eBooks · doi:10.1128/9781555817749.ch4 · Cited by 11
Enzyme evolution and the development of metabolic pathways
Peretó, J. G., Fani, R., Leguina, J., & Reyes, A. E. L. A. (1997) · Cited by 7
Current trends in the bioinformatic sequence analysis of metabolic pathways in prokaryotes
Brilli, M., Fani, R., & Liò, P. (2007) · Briefings Bioinform. · doi:10.1093/bib/bbm051 · Cited by 7
Phylogenetics and Computational Biology of Multigene Families
Lió, P., Brilli, M., & Fani, R. (2007) · Biological and medical physics series · doi:10.1007/978-3-540-35306-5_9 · Cited by 3
Activation of cam promoterless gene by ISR10 transposition in an Escherichia coli population under stress conditions
Lioy, M., Dabizzi, S., Ammannato, S., Caciotti, A., Cioni, L., & Fani, R. (2001) · Florence Research (University of Florence) · Cited by 2
The enhancement activities of histidyl-histidine in some prebiotic reactions.
Shen, C., Lazcano, A., & Oro, J. (1990) · PubMed · doi:10.1007/bf02102070 · Cited by 2

Sorted by citations

Regulation and function of the mammalian tricarboxylic acid cycle
Arnold, P. K., & Finley, L. W. S. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102838 · Cited by 535
“Being able to finetune the function of metabolic pathways like the TCA cycle —in particular, to toggle between catabolic and anabolic activity—set the stage for early unicellular life forms to evolve into multicellular organisms, which require coordination of metabolic activity beyond that dictated by local nutrient a…”
Background
The Rise of Chemodiversity in Plants
Weng, J., Philippe, R. N., & Noel, J. P. (2012) · Science · doi:10.1126/science.1217411 · Cited by 428
Origin and evolution of transporter substrate specificity within the NPF family
Jørgensen, M. E., Xu, D., Crocoll, C., Ernst, H. A., Ramírez, D., Motawia, M. S., Olsen, C. E., Mirza, O., Nour‐Eldin, H. H., & Halkier, B. A. (2017) · eLife · doi:10.7554/elife.19466 · Cited by 116
Xenogeneic Silencing and Its Impact on Bacterial Genomes
Singh, K., Milstein, J. N., & Navarre, W. W. (2016) · Annual Review of Microbiology · doi:10.1146/annurev-micro-102215-095301 · Cited by 95
Origin and evolution of operons and metabolic pathways
Fondi, M., Emiliani, G., & Fani, R. (2009) · Research in Microbiology · doi:10.1016/j.resmic.2009.05.001 · Cited by 83

See all 117

Authors: Fani, R., & Fondi, M.
Affiliations: University of Florence (IT)
Corresponding author: Fani, Renato
ORCID: Fani, Renato
Fondi, Marco
Venue: Physics of Life Reviews
Publisher: Elsevier BV
Published: 2009-03
Volume: 6
Issue: 1
Pages: 23-52
ISSN: 1571-0645 (ISSN-L)
DOI: 10.1016/j.plrev.2008.12.003
OpenAlex: W1974232498
Cited by: 117
References: 135
Citations by year: 2026: 1 · 2025: 8 · 2024: 7 · 2023: 12 · 2022: 7 · 2021: 9 · 2020: 7 · 2019: 7 · 2018: 6 · 2017: 5 · 2016: 4 · 2015: 4 · 2014: 7 · 2013: 9 · 2012: 7
FWCI: 4.04
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Physics of Life Reviews (publishedVersion)
PubMed (publishedVersion)
Florence Research (University of Florence) (submittedVersion)
Topics: Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: origin of metabolism, metabolic pathway evolution, gene duplication, histidine biosynthesis, nitrogen fixation, heterotrophy, genome evolution, archaea, bacteria, eukaryotes

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Origin and evolution of metabolic pathways

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks