1
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Todd BP, Downard KM. Structural Phylogenetics with Protein Mass Spectrometry: A Proof-of-Concept. Protein J 2024:10.1007/s10930-024-10227-8. [PMID: 39078529 DOI: 10.1007/s10930-024-10227-8] [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] [Accepted: 07/18/2024] [Indexed: 07/31/2024]
Abstract
It is demonstrated, for the first time, that a mass spectrometry approach (known as phylonumerics) can be successfully implemented for structural phylogenetics investigations to chart the evolution of a protein's structure and function. Illustrated for the compact globular protein myoglobin, peptide masses produced from the proteolytic digestion of the protein across animal species generate trees congruent to the sequence tree counterparts. Single point mutations calculated during the same mass tree building step can be followed along interconnected branches of the tree and represent a viable structural metric. A mass tree built for 15 diverse animal species, easily resolve the birds from mammal species, and the ruminant mammals from the remainder of the animals. Mutations within helix-spanning peptide segments alter both the mass and structure of the protein in these segments. Greater evolution is found in the B-helix over the A, E, F, G and H helices. A further mass tree study, of six more closely related primate species, resolves gorilla from the other primates based on a P22S mutation within the B-helix. The remaining five primates are resolved into two groups based on whether they contain a glycine or serine at position 23 in the same helix. The orangutan is resolved from the gibbon and siamang by its G-helix C110S mutation, while homo sapiens are resolved from chimpanzee based on the Q116H mutation. All are associated with structural perturbations in such helices. These structure altering mutations can be tracked along interconnecting branches of a mass tree, to follow the protein's structure and evolution, and ultimately the evolution of the species in which the proteins are expressed. Those that have the greatest impact on a protein's structure, its function, and ultimately the evolution of the species, can be selectively tracked or monitored.
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Affiliation(s)
- Benjamin P Todd
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia.
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2
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Gaschignard G, Millet M, Bruley A, Benzerara K, Dezi M, Skouri-Panet F, Duprat E, Callebaut I. AlphaFold2-guided description of CoBaHMA, a novel family of bacterial domains within the heavy-metal-associated superfamily. Proteins 2024; 92:776-794. [PMID: 38258321 DOI: 10.1002/prot.26668] [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] [Received: 09/28/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024]
Abstract
Three-dimensional (3D) structure information, now available at the proteome scale, may facilitate the detection of remote evolutionary relationships in protein superfamilies. Here, we illustrate this with the identification of a novel family of protein domains related to the ferredoxin-like superfold, by combining (i) transitive sequence similarity searches, (ii) clustering approaches, and (iii) the use of AlphaFold2 3D structure models. Domains of this family were initially identified in relation with the intracellular biomineralization of calcium carbonates by Cyanobacteria. They are part of the large heavy-metal-associated (HMA) superfamily, departing from the latter by specific sequence and structural features. In particular, most of them share conserved basic amino acids (hence their name CoBaHMA for Conserved Basic residues HMA), forming a positively charged surface, which is likely to interact with anionic partners. CoBaHMA domains are found in diverse modular organizations in bacteria, existing in the form of monodomain proteins or as part of larger proteins, some of which are membrane proteins involved in transport or lipid metabolism. This suggests that the CoBaHMA domains may exert a regulatory function, involving interactions with anionic lipids. This hypothesis might have a particular resonance in the context of the compartmentalization observed for cyanobacterial intracellular calcium carbonates.
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Affiliation(s)
- Geoffroy Gaschignard
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Maxime Millet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Apolline Bruley
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Manuela Dezi
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Feriel Skouri-Panet
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Elodie Duprat
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
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3
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Cifuente JO, Colleoni C, Kalscheuer R, Guerin ME. Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes. Chem Rev 2024; 124:4863-4934. [PMID: 38606812 PMCID: PMC11046441 DOI: 10.1021/acs.chemrev.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.
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Affiliation(s)
- Javier O. Cifuente
- Instituto
Biofisika (UPV/EHU, CSIC), University of
the Basque Country, E-48940 Leioa, Spain
| | - Christophe Colleoni
- University
of Lille, CNRS, UMR8576-UGSF -Unité de Glycobiologie Structurale
et Fonctionnelle, F-59000 Lille, France
| | - Rainer Kalscheuer
- Institute
of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, 40225 Dusseldorf, Germany
| | - Marcelo E. Guerin
- Structural
Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish
National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028 Barcelona, Catalonia, Spain
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4
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Caetano-Anollés K, Aziz MF, Mughal F, Caetano-Anollés G. On Protein Loops, Prior Molecular States and Common Ancestors of Life. J Mol Evol 2024:10.1007/s00239-024-10167-y. [PMID: 38652291 DOI: 10.1007/s00239-024-10167-y] [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: 02/05/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024]
Abstract
The principle of continuity demands the existence of prior molecular states and common ancestors responsible for extant macromolecular structure. Here, we focus on the emergence and evolution of loop prototypes - the elemental architects of protein domain structure. Phylogenomic reconstruction spanning superkingdoms and viruses generated an evolutionary chronology of prototypes with six distinct evolutionary phases defining a most parsimonious evolutionary progression of cellular life. Each phase was marked by strategic prototype accumulation shaping the structures and functions of common ancestors. The last universal common ancestor (LUCA) of cells and viruses and the last universal cellular ancestor (LUCellA) defined stem lines that were structurally and functionally complex. The evolutionary saga highlighted transformative forces. LUCA lacked biosynthetic ribosomal machinery, while the pivotal LUCellA lacked essential DNA biosynthesis and modern transcription. Early proteins therefore relied on RNA for genetic information storage but appeared initially decoupled from it, hinting at transformative shifts of genetic processing. Urancestral loop types suggest advanced folding designs were present at an early evolutionary stage. An exploration of loop geometric properties revealed gradual replacement of prototypes with α-helix and β-strand bracing structures over time, paving the way for the dominance of other loop types. AlphFold2-generated atomic models of prototype accretion described patterns of fold emergence. Our findings favor a ‛processual' model of evolving stem lines aligned with Woese's vision of a communal world. This model prompts discussing the 'problem of ancestors' and the challenges that lie ahead for research in taxonomy, evolution and complexity.
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Affiliation(s)
- Kelsey Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Callout Biotech, Albuquerque, NM, 87112, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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5
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Romei M, Carpentier M, Chomilier J, Lecointre G. Origins and Functional Significance of Eukaryotic Protein Folds. J Mol Evol 2023; 91:854-864. [PMID: 38060007 DOI: 10.1007/s00239-023-10136-x] [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] [Received: 02/27/2023] [Accepted: 10/03/2023] [Indexed: 12/08/2023]
Abstract
Folds are the architecture and topology of a protein domain. Categories of folds are very few compared to the astronomical number of sequences. Eukaryotes have more protein folds than Archaea and Bacteria. These folds are of two types: shared with Archaea and/or Bacteria on one hand and specific to eukaryotic clades on the other hand. The first kind of folds is inherited from the first endosymbiosis and confirms the mixed origin of eukaryotes. In a dataset of 1073 folds whose presence or absence has been evidenced among 210 species equally distributed in the three super-kingdoms, we have identified 28 eukaryotic folds unambiguously inherited from Bacteria and 40 eukaryotic folds unambiguously inherited from Archaea. Compared to previous studies, the repartition of informational function is higher than expected for folds originated from Bacteria and as high as expected for folds inherited from Archaea. The second type of folds is specifically eukaryotic and associated with an increase of new folds within eukaryotes distributed in particular clades. Reconstructed ancestral states coupled with dating of each node on the tree of life provided fold appearance rates. The rate is on average twice higher within Eukaryota than within Bacteria or Archaea. The highest rates are found in the origins of eukaryotes, holozoans, metazoans, metazoans stricto sensu, and vertebrates: the roots of these clades correspond to bursts of fold evolution. We could correlate the functions of some of the fold synapomorphies within eukaryotes with significant evolutionary events. Among them, we find evidence for the rise of multicellularity, adaptive immune system, or virus folds which could be linked to an ecological shift made by tetrapods.
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Affiliation(s)
- Martin Romei
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
- IMPMC (UMR 7590), BiBiP, Sorbonne Université, CNRS, MNHN, Paris, France
| | - Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France.
| | - Jacques Chomilier
- IMPMC (UMR 7590), BiBiP, Sorbonne Université, CNRS, MNHN, Paris, France
| | - Guillaume Lecointre
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205), Sorbonne Université, MNHN, CNRS, EPHE, UA, Paris, France
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6
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Mughal F, Caetano-Anollés G. Evolution of Intrinsic Disorder in Protein Loops. Life (Basel) 2023; 13:2055. [PMID: 37895436 PMCID: PMC10608553 DOI: 10.3390/life13102055] [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: 09/13/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Intrinsic disorder accounts for the flexibility of protein loops, molecular building blocks that are largely responsible for the processes and molecular functions of the living world. While loops likely represent early structural forms that served as intermediates in the emergence of protein structural domains, their origin and evolution remain poorly understood. Here, we conduct a phylogenomic survey of disorder in loop prototypes sourced from the ArchDB classification. Tracing prototypes associated with protein fold families along an evolutionary chronology revealed that ancient prototypes tended to be more disordered than their derived counterparts, with ordered prototypes developing later in evolution. This highlights the central evolutionary role of disorder and flexibility. While mean disorder increased with time, a minority of ordered prototypes exist that emerged early in evolutionary history, possibly driven by the need to preserve specific molecular functions. We also revealed the percolation of evolutionary constraints from higher to lower levels of organization. Percolation resulted in trade-offs between flexibility and rigidity that impacted prototype structure and geometry. Our findings provide a deep evolutionary view of the link between structure, disorder, flexibility, and function, as well as insights into the evolutionary role of intrinsic disorder in loops and their contribution to protein structure and function.
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Affiliation(s)
- Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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7
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Malik AJ, Langer D, Verma CS, Poole AM, Allison JR. Structome: a tool for the rapid assembly of datasets for structural phylogenetics. BIOINFORMATICS ADVANCES 2023; 3:vbad134. [PMID: 38046099 PMCID: PMC10692761 DOI: 10.1093/bioadv/vbad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/17/2023] [Accepted: 09/29/2023] [Indexed: 12/05/2023]
Abstract
Summary Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed that allows users to rapidly identify protein structures similar to a query protein and to assemble datasets useful for structure-based phylogenetics. Structome was created by clustering ∼ 94 % of the structures in RCSB PDB using 90% sequence identity and representing each cluster by a centroid structure. Structure similarity between centroid proteins was calculated, and annotations from PDB, SCOP, and CATH were integrated. To illustrate utility, an H3 histone was used as a query, and results show that the protein structures returned by Structome span both sequence and structural diversity of the histone fold. Additionally, the pre-computed nexus-formatted distance matrix, provided by Structome, enables analysis of evolutionary relationships between proteins not identifiable using searches based on sequence similarity alone. Our results demonstrate that, beginning with a single structure, Structome can be used to rapidly generate a dataset of structural neighbours and allows deep evolutionary history of proteins to be studied. Availability and Implementation Structome is available at: https://structome.bii.a-star.edu.sg.
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Affiliation(s)
- Ashar J Malik
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 138671 Singapore
| | - Desiree Langer
- School of Biological Sciences, University of Auckland, 1142 Auckland, New Zealand
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 138671 Singapore
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, 1142 Auckland, New Zealand
- Digital Life Institute, University of Auckland, Auckland 1142, New Zealand
| | - Jane R Allison
- School of Biological Sciences, University of Auckland, 1142 Auckland, New Zealand
- Digital Life Institute, University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1142 Auckland, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, 8041 Christchurch, New Zealand
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8
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Aziz MF, Mughal F, Caetano-Anollés G. Tracing the birth of structural domains from loops during protein evolution. Sci Rep 2023; 13:14688. [PMID: 37673948 PMCID: PMC10482863 DOI: 10.1038/s41598-023-41556-w] [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] [Received: 12/25/2022] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
The structures and functions of proteins are embedded into the loop scaffolds of structural domains. Their origin and evolution remain mysterious. Here, we use a novel graph-theoretical approach to describe how modular and non-modular loop prototypes combine to form folded structures in protein domain evolution. Phylogenomic data-driven chronologies reoriented a bipartite network of loops and domains (and its projections) into 'waterfalls' depicting an evolving 'elementary functionome' (EF). Two primordial waves of functional innovation involving founder 'p-loop' and 'winged-helix' domains were accompanied by an ongoing emergence and reuse of structural and functional novelty. Metabolic pathways expanded before translation functionalities. A dual hourglass recruitment pattern transferred scale-free properties from loop to domain components of the EF network in generative cycles of hierarchical modularity. Modeling the evolutionary emergence of the oldest P-loop and winged-helix domains with AlphFold2 uncovered rapid convergence towards folded structure, suggesting that a folding vocabulary exists in loops for protein fold repurposing and design.
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Affiliation(s)
- M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA.
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9
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Caetano-Anollés G. Agency in evolution of biomolecular communication. Ann N Y Acad Sci 2023; 1525:88-103. [PMID: 37219369 DOI: 10.1111/nyas.15005] [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: 05/24/2023]
Abstract
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an organized system of signs-a communicative agency-for creating and transmitting meaning. The emergence of agency, the capacity to act in a given context and generate end-directed behaviors, has baffled evolutionary biologists for centuries. Here, I explore its emergence with knowledge grounded in over two decades of evolutionary genomic and bioinformatic exploration. Biphasic processes of growth and diversification exist that generate hierarchy and modularity in biological systems at widely ranging time scales. Similarly, a biphasic process exists in communication that constructs a message before it can be transmitted for interpretation. Transmission dissipates matter-energy and information and involves computation. Agency emerges when molecular machinery generates hierarchical layers of vocabularies in an entangled communication network clustered around the universal Turing machine of the ribosome. Computations canalize biological systems to perform biological functions in a dissipative quest to structure long-lived occurrents. This occurs within the confines of a "triangle of persistence" that maximizes invariance with trade-offs between economy, flexibility, and robustness. Thus, learning from previous historical and circumstantial experiences unifies modules in a hierarchy that expands the agency of systems.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences and C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
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10
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Romei M, Sapriel G, Imbert P, Jamay T, Chomilier J, Lecointre G, Carpentier M. Protein folds as synapomorphies of the tree of life. Evolution 2022; 76:1706-1719. [PMID: 35765784 PMCID: PMC9541633 DOI: 10.1111/evo.14550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 01/22/2023]
Abstract
Several studies showed that folds (topology of protein secondary structures) distribution in proteomes may be a global proxy to build phylogeny. Then, some folds should be synapomorphies (derived characters exclusively shared among taxa). However, previous studies used methods that did not allow synapomorphy identification, which requires congruence analysis of folds as individual characters. Here, we map SCOP folds onto a sample of 210 species across the tree of life (TOL). Congruence is assessed using retention index of each fold for the TOL, and principal component analysis for deeper branches. Using a bicluster mapping approach, we define synapomorphic blocks of folds (SBF) sharing similar presence/absence patterns. Among the 1232 folds, 20% are universally present in our TOL, whereas 54% are reliable synapomorphies. These results are similar with CATH and ECOD databases. Eukaryotes are characterized by a large number of them, and several SBFs clearly support nested eukaryotic clades (divergence times from 1100 to 380 mya). Although clearly separated, the three superkingdoms reveal a strong mosaic pattern. This pattern is consistent with the dual origin of eukaryotes and witness secondary endosymbiosis in their phothosynthetic clades. Our study unveils direct analysis of folds synapomorphies as key characters to unravel evolutionary history of species.
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Affiliation(s)
- Martin Romei
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance,IMPMC (UMR 7590), BiBiP, Sorbonne Université, CNRS, MNHNParisFrance
| | - Guillaume Sapriel
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance,UFR des sciences de la santéUniversité Versailles‐St‐QuentinVersaillesFrance
| | - Pierre Imbert
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
| | - Théo Jamay
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
| | | | - Guillaume Lecointre
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
| | - Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB UMR 7205)Sorbonne Université, MNHN, CNRS, EPHE, UAParisFrance
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11
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The Legend of ATP: From Origin of Life to Precision Medicine. Metabolites 2022; 12:metabo12050461. [PMID: 35629965 PMCID: PMC9148104 DOI: 10.3390/metabo12050461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 02/05/2023] Open
Abstract
Adenosine triphosphate (ATP) may be the most important biological small molecule. Since it was discovered in 1929, ATP has been regarded as life’s energy reservoir. However, this compound means more to life. Its legend starts at the dawn of life and lasts to this day. ATP must be the basic component of ancient ribozymes and may facilitate the origin of structured proteins. In the existing organisms, ATP continues to construct ribonucleic acid (RNA) and work as a protein cofactor. ATP also functions as a biological hydrotrope, which may keep macromolecules soluble in the primitive environment and can regulate phase separation in modern cells. These functions are involved in the pathogenesis of aging-related diseases and breast cancer, providing clues to discovering anti-aging agents and precision medicine tactics for breast cancer.
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12
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Aledo JC. Phylogenies from unaligned proteomes using sequence environments of amino acid residues. Sci Rep 2022; 12:7497. [PMID: 35523825 PMCID: PMC9076898 DOI: 10.1038/s41598-022-11370-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/21/2022] [Indexed: 11/09/2022] Open
Abstract
Alignment-free methods for sequence comparison and phylogeny inference have attracted a great deal of attention in recent years. Several algorithms have been implemented in diverse software packages. Despite the great number of existing methods, most of them are based on word statistics. Although they propose different filtering and weighting strategies and explore different metrics, their performance may be limited by the phylogenetic signal preserved in these words. Herein, we present a different approach based on the species-specific amino acid neighborhood preferences. These differential preferences can be assessed in the context of vector spaces. In this way, a distance-based method to build phylogenies has been developed and implemented into an easy-to-use R package. Tests run on real-world datasets show that this method can reconstruct phylogenetic relationships with high accuracy, and often outperforms other alignment-free approaches. Furthermore, we present evidence that the new method can perform reliably on datasets formed by non-orthologous protein sequences, that is, the method not only does not require the identification of orthologous proteins, but also does not require their presence in the analyzed dataset. These results suggest that the neighborhood preference of amino acids conveys a phylogenetic signal that may be of great utility in phylogenomics.
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Affiliation(s)
- Juan Carlos Aledo
- Department of Molecular Biology and Biochemistry, University of Málaga, 29071, Málaga, Spain.
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13
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Caetano-Anollés G, Aziz MF, Mughal F, Caetano-Anollés D. Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution. Expert Rev Proteomics 2021; 18:863-880. [PMID: 34628994 DOI: 10.1080/14789450.2021.1992277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and proteomes. Molecular chronologies are series of time events describing the history of biological systems and subsystems and the rise of biological innovations. Together with time-varying networks, these chronologies provide a window into the past. AREAS COVERED Here, we review molecular chronologies and networks built with modern methods of phylogeny reconstruction. We discuss how chronologies of structural domain families uncover the explosive emergence of metabolism, the late rise of translation, the co-evolution of ribosomal proteins and rRNA, and the late development of the ribosomal exit tunnel; events that coincided with a tendency to shorten folding time. Evolving networks described the early emergence of domains and a late 'big bang' of domain combinations. EXPERT OPINION Two processes, folding and recruitment appear central to the evolutionary progression. The former increases protein persistence. The later fosters diversity. Chronologically, protein evolution mirrors folding by combining supersecondary structures into domains, developing translation machinery to facilitate folding speed and stability, and enhancing structural complexity by establishing long-distance interactions in novel structural and architectural designs.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA.,C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, Illinois, USA
| | - Derek Caetano-Anollés
- Data Science Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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14
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Caetano-Anollés G. The Compressed Vocabulary of Microbial Life. Front Microbiol 2021; 12:655990. [PMID: 34305827 PMCID: PMC8292947 DOI: 10.3389/fmicb.2021.655990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Communication is an undisputed central activity of life that requires an evolving molecular language. It conveys meaning through messages and vocabularies. Here, I explore the existence of a growing vocabulary in the molecules and molecular functions of the microbial world. There are clear correspondences between the lexicon, syntax, semantics, and pragmatics of language organization and the module, structure, function, and fitness paradigms of molecular biology. These correspondences are constrained by universal laws and engineering principles. Macromolecular structure, for example, follows quantitative linguistic patterns arising from statistical laws that are likely universal, including the Zipf's law, a special case of the scale-free distribution, the Heaps' law describing sublinear growth typical of economies of scales, and the Menzerath-Altmann's law, which imposes size-dependent patterns of decreasing returns. Trade-off solutions between principles of economy, flexibility, and robustness define a "triangle of persistence" describing the impact of the environment on a biological system. The pragmatic landscape of the triangle interfaces with the syntax and semantics of molecular languages, which together with comparative and evolutionary genomic data can explain global patterns of diversification of cellular life. The vocabularies of proteins (proteomes) and functions (functionomes) revealed a significant universal lexical core supporting a universal common ancestor, an ancestral evolutionary link between Bacteria and Eukarya, and distinct reductive evolutionary strategies of language compression in Archaea and Bacteria. A "causal" word cloud strategy inspired by the dependency grammar paradigm used in catenae unfolded the evolution of lexical units associated with Gene Ontology terms at different levels of ontological abstraction. While Archaea holds the smallest, oldest, and most homogeneous vocabulary of all superkingdoms, Bacteria heterogeneously apportions a more complex vocabulary, and Eukarya pushes functional innovation through mechanisms of flexibility and robustness.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, and C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
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15
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Abstract
Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. A time series of networks revealed two ancient waves of structural novelty arising from ancient 'p-loop' and 'winged helix' domains and a massive 'big bang' of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity showed yin-and-yang complementary transition and biphasic patterns along the structural chronology. Remarkably, the evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.
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16
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Ibrahim A, Colson P, Merhej V, Zgheib R, Maatouk M, Naud S, Bittar F, Raoult D. Rhizomal Reclassification of Living Organisms. Int J Mol Sci 2021; 22:5643. [PMID: 34073251 PMCID: PMC8199106 DOI: 10.3390/ijms22115643] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/14/2021] [Accepted: 05/23/2021] [Indexed: 12/11/2022] Open
Abstract
Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.
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Affiliation(s)
- Ahmad Ibrahim
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Vicky Merhej
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Rita Zgheib
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, SSA, VITROME, 13005 Marseille, France
| | - Mohamad Maatouk
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Sabrina Naud
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Fadi Bittar
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 13005 Marseille, France; (A.I.); (P.C.); (V.M.); (R.Z.); (M.M.); (S.N.)
- Aix-Marseille Université, IRD, APHM, MEPHI, 13005 Marseille, France
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17
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Nasir A, Mughal F, Caetano-Anollés G. The tree of life describes a tripartite cellular world. Bioessays 2021; 43:e2000343. [PMID: 33837594 DOI: 10.1002/bies.202000343] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 12/28/2022]
Abstract
The canonical view of a 3-domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2-domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment-dependent approaches, which often fail to satisfactorily address the problem of ''gaps.'' In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment-free methodologies lift most difficulties but require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here: https://youtu.be/-6TBN0bubI8.
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Affiliation(s)
- Arshan Nasir
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Fizza Mughal
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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18
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Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods 2021; 18:366-368. [PMID: 33828273 PMCID: PMC8026399 DOI: 10.1038/s41592-021-01101-x] [Citation(s) in RCA: 1051] [Impact Index Per Article: 350.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 02/22/2021] [Indexed: 12/05/2022]
Abstract
We are at the beginning of a genomic revolution in which all known species are planned to be sequenced. Accessing such data for comparative analyses is crucial in this new age of data-driven biology. Here, we introduce an improved version of DIAMOND that greatly exceeds previous search performances and harnesses supercomputing to perform tree-of-life scale protein alignments in hours, while matching the sensitivity of the gold standard BLASTP. An updated version of DIAMOND uses improved algorithmic procedures and a customized high-performance computing framework to make seemingly prohibitive large-scale protein sequence alignments feasible.
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19
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Dalhoff A. Selective toxicity of antibacterial agents-still a valid concept or do we miss chances and ignore risks? Infection 2021; 49:29-56. [PMID: 33367978 PMCID: PMC7851017 DOI: 10.1007/s15010-020-01536-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Selective toxicity antibacteribiotics is considered to be due to interactions with targets either being unique to bacteria or being characterized by a dichotomy between pro- and eukaryotic pathways with high affinities of agents to bacterial- rather than eukaryotic targets. However, the theory of selective toxicity oversimplifies the complex modes of action of antibiotics in pro- and eukaryotes. METHODS AND OBJECTIVE This review summarizes data describing multiple modes of action of antibiotics in eukaryotes. RESULTS Aminoglycosides, macrolides, oxazolidinones, chloramphenicol, clindamycin, tetracyclines, glycylcyclines, fluoroquinolones, rifampicin, bedaquillin, ß-lactams inhibited mitochondrial translation either due to binding to mitosomes, inhibition of mitochondrial RNA-polymerase-, topoisomerase 2ß-, ATP-synthesis, transporter activities. Oxazolidinones, tetracyclines, vancomycin, ß-lactams, bacitracin, isoniazid, nitroxoline inhibited matrix-metalloproteinases (MMP) due to chelation with zinc and calcium, whereas fluoroquinols fluoroquinolones and chloramphenicol chelated with these cations, too, but increased MMP activities. MMP-inhibition supported clinical efficacies of ß-lactams and daptomycin in skin-infections, and of macrolides, tetracyclines in respiratory-diseases. Chelation may have contributed to neuroprotection by ß-lactams and fluoroquinolones. Aminoglycosides, macrolides, chloramphenicol, oxazolidins oxazolidinones, tetracyclines caused read-through of premature stop codons. Several additional targets for antibiotics in human cells have been identified like interaction of fluoroquinolones with DNA damage repair in eukaryotes, or inhibition of mucin overproduction by oxazolidinones. CONCLUSION The effects of antibiotics on eukaryotes are due to identical mechanisms as their antibacterial activities because of structural and functional homologies of pro- and eukaryotic targets, so that the effects of antibiotics on mammals are integral parts of their overall mechanisms of action.
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Affiliation(s)
- Axel Dalhoff
- Christian-Albrechts-University of Kiel, Institue for Infection Medicine, Brunswiker Str. 4, D-24105, Kiel, Germany.
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20
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Yazhini A, Srinivasan N, Sandhya S. Signatures of conserved and unique molecular features in Afrotheria. Sci Rep 2021; 11:1011. [PMID: 33441654 PMCID: PMC7806701 DOI: 10.1038/s41598-020-79559-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 12/07/2020] [Indexed: 11/09/2022] Open
Abstract
Afrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.
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Affiliation(s)
- Arangasamy Yazhini
- Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Narayanaswamy Srinivasan
- Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
| | - Sankaran Sandhya
- Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
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21
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Colson P, Pinault L, Azza S, Armstrong N, Chabriere E, La Scola B, Pontarotti P, Raoult D. A protein of the metallo-hydrolase/oxidoreductase superfamily with both beta-lactamase and ribonuclease activity is linked with translation in giant viruses. Sci Rep 2020; 10:21685. [PMID: 33303919 PMCID: PMC7729979 DOI: 10.1038/s41598-020-78658-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/23/2020] [Indexed: 12/21/2022] Open
Abstract
Proteins with a metallo-beta-lactamase (MBL) fold have been largely studied in bacteria in the framework of resistance to beta-lactams, but their spectrum of activities is broader. We show here that the giant Tupanvirus also encodes a MBL fold-protein that has orthologs in other giant viruses, a deep phylogenetic root and is clustered with tRNases. This protein is significantly associated with translation components in giant viruses. After expression in Escherichia coli, it was found to hydrolyse nitrocefin, a beta-lactam, and penicillin G. This was inhibited by sulbactam, a beta-lactamase inhibitor. In addition, the tupanvirus MBL fold-protein was not active on single- or double-stranded DNA, but degraded RNAs from bacteria and Acanthamoeba castellanii, the tupanvirus amoebal host. This activity was not neutralized by sulbactam. Overall, our results still broaden the host range of MBL fold-proteins, showing dual beta-lactamase/nuclease activities in giant viruses.
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Affiliation(s)
- Philippe Colson
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Lucile Pinault
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Said Azza
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Nicholas Armstrong
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Chabriere
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre Pontarotti
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.,CNRS, Marseille, France
| | - Didier Raoult
- Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France. .,IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
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22
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Yadav A, Fernández-Baca D, Cannon SB. Family-Specific Gains and Losses of Protein Domains in the Legume and Grass Plant Families. Evol Bioinform Online 2020; 16:1176934320939943. [PMID: 32694909 PMCID: PMC7350399 DOI: 10.1177/1176934320939943] [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: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 11/27/2022] Open
Abstract
Protein domains can be regarded as sections of protein sequences capable of folding independently and performing specific functions. In addition to amino-acid level changes, protein sequences can also evolve through domain shuffling events such as domain insertion, deletion, or duplication. The evolution of protein domains can be studied by tracking domain changes in a selected set of species with known phylogenetic relationships. Here, we conduct such an analysis by defining domains as “features” or “descriptors,” and considering the species (target + outgroup) as instances or data-points in a data matrix. We then look for features (domains) that are significantly different between the target species and the outgroup species. We study the domain changes in 2 large, distinct groups of plant species: legumes (Fabaceae) and grasses (Poaceae), with respect to selected outgroup species. We evaluate 4 types of domain feature matrices: domain content, domain duplication, domain abundance, and domain versatility. The 4 types of domain feature matrices attempt to capture different aspects of domain changes through which the protein sequences may evolve—that is, via gain or loss of domains, increase or decrease in the copy number of domains along the sequences, expansion or contraction of domains, or through changes in the number of adjacent domain partners. All the feature matrices were analyzed using feature selection techniques and statistical tests to select protein domains that have significant different feature values in legumes and grasses. We report the biological functions of the top selected domains from the analysis of all the feature matrices. In addition, we also perform domain-centric gene ontology (dcGO) enrichment analysis on all selected domains from all 4 feature matrices to study the gene ontology terms associated with the significantly evolving domains in legumes and grasses. Domain content analysis revealed a striking loss of protein domains from the Fanconi anemia (FA) pathway, the pathway responsible for the repair of interstrand DNA crosslinks. The abundance analysis of domains found in legumes revealed an increase in glutathione synthase enzyme, an antioxidant required from nitrogen fixation, and a decrease in xanthine oxidizing enzymes, a phenomenon confirmed by previous studies. In grasses, the abundance analysis showed increases in domains related to gene silencing which could be due to polyploidy or due to enhanced response to viral infection. We provide a docker container that can be used to perform this analysis workflow on any user-defined sets of species, available at https://cloud.docker.com/u/akshayayadav/repository/docker/akshayayadav/protein-domain-evolution-project.
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Affiliation(s)
- Akshay Yadav
- Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, USA
| | | | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, USA
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23
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Chu XY, Zhang HY. Cofactors as Molecular Fossils To Trace the Origin and Evolution of Proteins. Chembiochem 2020; 21:3161-3168. [PMID: 32515532 DOI: 10.1002/cbic.202000027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Due to their early origin and extreme conservation, cofactors are valuable molecular fossils for tracing the origin and evolution of proteins. First, as the order of protein folds binding with cofactors roughly coincides with protein-fold chronology, cofactors are considered to have facilitated the origin of primitive proteins by selecting them from pools of random amino acid sequences. Second, in the subsequent evolution of proteins, cofactors still played an important role. More interestingly, as metallic cofactors evolved with geochemical variations, some geochemical events left imprints in the chronology of protein architecture; this provides further evidence supporting the coevolution of biochemistry and geochemistry. In this paper, we attempt to review the molecular fossils used in tracing the origin and evolution of proteins, with a special focus on cofactors.
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Affiliation(s)
- Xin-Yi Chu
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
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24
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Williams TA, Cox CJ, Foster PG, Szöllősi GJ, Embley TM. Phylogenomics provides robust support for a two-domains tree of life. Nat Ecol Evol 2020; 4:138-147. [PMID: 31819234 PMCID: PMC6942926 DOI: 10.1038/s41559-019-1040-x] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/15/2019] [Indexed: 11/09/2022]
Abstract
Hypotheses about the origin of eukaryotic cells are classically framed within the context of a universal 'tree of life' based on conserved core genes. Vigorous ongoing debate about eukaryote origins is based on assertions that the topology of the tree of life depends on the taxa included and the choice and quality of genomic data analysed. Here we have reanalysed the evidence underpinning those claims and apply more data to the question by using supertree and coalescent methods to interrogate >3,000 gene families in archaea and eukaryotes. We find that eukaryotes consistently originate from within the archaea in a two-domains tree when due consideration is given to the fit between model and data. Our analyses support a close relationship between eukaryotes and Asgard archaea and identify the Heimdallarchaeota as the current best candidate for the closest archaeal relatives of the eukaryotic nuclear lineage.
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Affiliation(s)
- Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Cymon J Cox
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, UK
| | - Gergely J Szöllősi
- MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Budapest, Hungary
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- Evolutionary Systems Research Group, Centre for Ecological Research, Hungarian Academy of Sciences, Tihany, Hungary
| | - T Martin Embley
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, UK.
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25
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Mughal F, Caetano-Anollés G. MANET 3.0: Hierarchy and modularity in evolving metabolic networks. PLoS One 2019; 14:e0224201. [PMID: 31648227 PMCID: PMC6812854 DOI: 10.1371/journal.pone.0224201] [Citation(s) in RCA: 9] [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: 05/14/2019] [Accepted: 10/08/2019] [Indexed: 11/30/2022] Open
Abstract
Enzyme recruitment is a fundamental evolutionary driver of modern metabolism. We see evidence of recruitment at work in the metabolic Molecular Ancestry Networks (MANET) database, an online resource that integrates data from KEGG, SCOP and structural phylogenomic reconstruction. The database, which was introduced in 2006, traces the deep history of the structural domains of enzymes in metabolic pathways. Here we release version 3.0 of MANET, which updates data from KEGG and SCOP, links enzyme and PDB information with PDBsum, and traces evolutionary information of domains defined at fold family level of SCOP classification in metabolic subnetwork diagrams. Compared to SCOP folds used in the previous versions, fold families are cohesive units of functional similarity that are highly conserved at sequence level and offer a 10-fold increase of data entries. We surveyed enzymatic, functional and catalytic site distributions among superkingdoms showing that ancient enzymatic innovations followed a biphasic temporal pattern of diversification typical of module innovation. We grouped enzymatic activities of MANET into a hierarchical system of subnetworks and mesonetworks matching KEGG classification. The evolutionary growth of these modules of metabolic activity was studied using bipartite networks and their one-mode projections at enzyme, subnetwork and mesonetwork levels of organization. Evolving metabolic networks revealed patterns of enzyme sharing that transcended mesonetwork boundaries and supported the patchwork model of metabolic evolution. We also explored the scale-freeness, randomness and small-world properties of evolving networks as possible organizing principles of network growth and diversification. The network structure shows an increase in hierarchical modularity and scale-free behavior as metabolic networks unfold in evolutionary time. Remarkably, this evolutionary constraint on structure was stronger at lower levels of metabolic organization. Evolving metabolic structure reveals a 'principle of granularity', an evolutionary increase of the cohesiveness of lower-level parts of a hierarchical system. MANET is available at http://manet.illinois.edu.
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Affiliation(s)
- Fizza Mughal
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gustavo Caetano-Anollés
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Caetano-Anollés G, Aziz MF, Mughal F, Gräter F, Koç I, Caetano-Anollés K, Caetano-Anollés D. Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. Evol Bioinform Online 2019; 15:1176934319872980. [PMID: 31523127 PMCID: PMC6728656 DOI: 10.1177/1176934319872980] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 01/15/2023] Open
Abstract
Networks describe how parts associate with each other to form integrated systems which often have modular and hierarchical structure. In biology, network growth involves two processes, one that unifies and the other that diversifies. Here, we propose a biphasic (bow-tie) theory of module emergence. In the first phase, parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are often selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In the second phase, variants of the modules diversify and become new parts for a new generative cycle of higher level organization. The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels. Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism, elementary functionomes, and protein domain organization.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory,
Department of Crop Sciences, C.R. Woese Institute for Genomic Biology, and Illinois
Informatics Institute, University of Illinois, Urbana, IL, USA
| | - M Fayez Aziz
- Evolutionary Bioinformatics Laboratory,
Department of Crop Sciences, C.R. Woese Institute for Genomic Biology, and Illinois
Informatics Institute, University of Illinois, Urbana, IL, USA
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory,
Department of Crop Sciences, C.R. Woese Institute for Genomic Biology, and Illinois
Informatics Institute, University of Illinois, Urbana, IL, USA
| | - Frauke Gräter
- Heidelberg Institute for Theoretical
Studies, Heidelberg, Germany
| | - Ibrahim Koç
- Department of Molecular Biology and
Genetics, Gebze Technical University, Gebze, Turkey
| | - Kelsey Caetano-Anollés
- Division of Biomedical Informatics,
College of Medicine, Seoul National University, Seoul, Republic of Korea
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Solis AD. Reduced alphabet of prebiotic amino acids optimally encodes the conformational space of diverse extant protein folds. BMC Evol Biol 2019; 19:158. [PMID: 31362700 PMCID: PMC6668081 DOI: 10.1186/s12862-019-1464-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/19/2019] [Indexed: 11/10/2022] Open
Abstract
Background There is wide agreement that only a subset of the twenty standard amino acids existed prebiotically in sufficient concentrations to form functional polypeptides. We ask how this subset, postulated as {A,D,E,G,I,L,P,S,T,V}, could have formed structures stable enough to found metabolic pathways. Inspired by alphabet reduction experiments, we undertook a computational analysis to measure the structural coding behavior of sequences simplified by reduced alphabets. We sought to discern characteristics of the prebiotic set that would endow it with unique properties relevant to structure, stability, and folding. Results Drawing on a large dataset of single-domain proteins, we employed an information-theoretic measure to assess how well the prebiotic amino acid set preserves fold information against all other possible ten-amino acid sets. An extensive virtual mutagenesis procedure revealed that the prebiotic set excellently preserves sequence-dependent information regarding both backbone conformation and tertiary contact matrix of proteins. We observed that information retention is fold-class dependent: the prebiotic set sufficiently encodes the structure space of α/β and α + β folds, and to a lesser extent, of all-α and all-β folds. The prebiotic set appeared insufficient to encode the small proteins. Assessing how well the prebiotic set discriminates native vs. incorrect sequence-structure matches, we found that α/β and α + β folds exhibit more pronounced energy gaps with the prebiotic set than with nearly all alternatives. Conclusions The prebiotic set optimally encodes local backbone structures that appear in the folded environment and near-optimally encodes the tertiary contact matrix of extant proteins. The fold-class-specific patterns observed from our structural analysis confirm the postulated timeline of fold appearance in proteogenesis derived from proteomic sequence analyses. Polypeptides arising in a prebiotic environment will likely form α/β and α + β-like folds if any at all. We infer that the progressive expansion of the alphabet allowed the increased conformational stability and functional specificity of later folds, including all-α, all-β, and small proteins. Our results suggest that prebiotic sequences are amenable to mutations that significantly lower native conformational energies and increase discrimination amidst incorrect folds. This property may have assisted the genesis of functional proto-enzymes prior to the expansion of the full amino acid alphabet.
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Affiliation(s)
- Armando D Solis
- Biological Sciences Department, New York City College of Technology (City Tech), The City University of New York (CUNY), 285 Jay Street, Brooklyn, NY, 11201, USA.
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Caetano-Anollés D, Nasir A, Kim KM, Caetano-Anollés G. Testing Empirical Support for Evolutionary Models that Root the Tree of Life. J Mol Evol 2019; 87:131-142. [PMID: 30887086 PMCID: PMC6443624 DOI: 10.1007/s00239-019-09891-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
Abstract
Trees of life (ToLs) can only be rooted with direct methods that seek optimization of character state information in ingroup taxa. This involves optimizing phylogenetic tree, model and data in an exercise of reciprocal illumination. Rooted ToLs have been built from a census of protein structural domains in proteomes using two kinds of models. Fully-reversible models use standard-ordered (additive) characters and Wagner parsimony to generate unrooted trees of proteomes that are then rooted with Weston's generality criterion. Non-reversible models directly build rooted trees with unordered characters and asymmetric stepmatrices of transformation costs that penalize gain over loss of domains. Here, we test the empirical support for the evolutionary models with character state reconstruction methods using two published proteomic datasets. We show that the reversible models match reconstructed frequencies of character change and are faithful to the distribution of serial homologies in trees. In contrast, the non-reversible models go counter to trends in the data they must explain, attracting organisms with large proteomes to the base of the rooted trees while violating the triangle inequality of distances. This can lead to serious reconstruction inconsistencies that show model inadequacy. Our study highlights the aprioristic perils of disposing of countering evidence in natural history reconstruction.
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Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, Plön, Germany.
| | - Arshan Nasir
- Department of Biosciences, COMSATS University, Islamabad, 45550, Pakistan
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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29
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Colson P, Levasseur A, La Scola B, Sharma V, Nasir A, Pontarotti P, Caetano-Anollés G, Raoult D. Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes. Front Microbiol 2018; 9:2668. [PMID: 30538677 PMCID: PMC6277510 DOI: 10.3389/fmicb.2018.02668] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/18/2018] [Indexed: 12/20/2022] Open
Abstract
Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named ‘TRUC’ (for “Things Resisting Uncompleted Classifications”) alongside Bacteria, Archaea, and Eukarya. Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs). Hierarchical clustering analysis was performed based on a binary presence/absence matrix constructed using 727 informational COGs from cellular organisms. The presence/absence of ‘universal’ FSF domains was used to generate an unrooted maximum parsimony phylogenomic tree. Comparison of the gene content of a giant virus with those of a bacterium, an archaeon, and a eukaryote with small genomes was also performed. Overall, both cladistic analyses based on gene sequences of very central and ancient proteins and on highly conserved protein fold structures as well as phenetic analyses were congruent regarding the delineation of a fourth branch of microbes comprised by giant viruses. Giant viruses appeared as a basal group in the tree of all proteomes. A pangenome and core genome determined for Rickettsia bellii (bacteria), Methanomassiliicoccus luminyensis (archaeon), Encephalitozoon intestinalis (eukaryote), and Tupanvirus (giant virus) showed a substantial proportion of Tupanvirus genes that overlap with those of the cellular microbes. In addition, a substantial genome mosaicism was observed, with 51, 11, 8, and 0.2% of Tupanvirus genes best matching with viruses, eukaryota, bacteria, and archaea, respectively. Finally, we found that genes themselves may be subject to lateral sequence transfers. In summary, our data highlight the quantum leap between classical and giant viruses. Phylogenetic and phyletic analyses and the study of protein fold superfamilies confirm previous evidence of the existence of a fourth TRUC of life that includes giant viruses, and highlight its ancestrality and mosaicism. They also point out that best evolutionary representations for giant viruses and cellular microorganisms are rhizomes, and that sequence transfers rather than gene transfers have to be considered.
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Affiliation(s)
- Philippe Colson
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Vikas Sharma
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Pierre Pontarotti
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Centre National de la Recherche Scientifique, Marseille, France
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM); Microbes, Evolution, Phylogeny and Infection (MEΦI); Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
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30
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Chouhan BPS, Maimaiti S, Gade M, Laurino P. Rossmann-Fold Methyltransferases: Taking a "β-Turn" around Their Cofactor, S-Adenosylmethionine. Biochemistry 2018; 58:166-170. [PMID: 30406995 DOI: 10.1021/acs.biochem.8b00994] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methyltransferases (MTases) are superfamilies of enzymes that catalyze the transfer of a methyl group from S-adenosylmethionine (SAM), a nucleoside-based cofactor, to a wide variety of substrates such as DNA, RNA, proteins, small molecules, and lipids. Depending upon their structural features, the MTases can be further classified into different classes; we consider exclusively the largest class of MTases, the Rossmann-fold MTases. It has been shown that the nucleoside cofactor-binding Rossmann enzymes, particularly the nicotinamide adenine dinucleotide (NAD)-, flavin adenine dinucleotide (FAD)-, and SAM-binding MTases enzymes, share common binding motifs that include a Gly-rich loop region that interacts with the cofactor and a highly conserved acidic residue (Asp/Glu) that interacts with the ribose moiety of the cofactor. Here, we observe that the Gly-rich loop region of the Rossmann MTases adapts a specific type II' β-turn in the proximity of the cofactor (<4 Å), and it appears to be a key feature of these superfamilies. Additionally, we demonstrate that the conservation of this β-turn could play a critical role in the enzyme-cofactor interaction, thereby shedding new light on the structural conformation of the Gly-rich loop region from Rossmann MTases.
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Affiliation(s)
- Bhanu Pratap Singh Chouhan
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Shayida Maimaiti
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Madhuri Gade
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
| | - Paola Laurino
- Okinawa Institute of Science and Technology Graduate University , 1919-1 Tancha, Onna-son , Okinawa 904-0412 , Japan
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31
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Youkharibache P, Veretnik S, Li Q, Stanek KA, Mura C, Bourne PE. The Small β-Barrel Domain: A Survey-Based Structural Analysis. Structure 2018; 27:6-26. [PMID: 30393050 DOI: 10.1016/j.str.2018.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 11/27/2022]
Abstract
The small β-barrel (SBB) is an ancient protein structural domain characterized by extremes: it features a broad range of structural varieties, a deeply intricate evolutionary history, and it is associated with a bewildering array of cellular pathways. Here, we present a thorough, survey-based analysis of the structural properties of SBBs. We first consider the defining properties of the SBB, including various systems of nomenclature used to describe it, and we introduce the unifying concept of an "urfold." To begin elucidating how vast functional diversity can be achieved by a relatively simple domain, we explore the anatomy of the SBB and its representative structural variants. Many SBB proteins assemble into cyclic oligomers as the biologically functional units; these oligomers often bind RNA, and typically exhibit great quaternary structural plasticity (homomeric and heteromeric rings, variable subunit stoichiometries, etc.). We conclude with three themes that emerge from the rich structure ↔ function versatility of the SBB.
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Affiliation(s)
- Philippe Youkharibache
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Stella Veretnik
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
| | - Qingliang Li
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA
| | - Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA.
| | - Philip E Bourne
- National Center for Biotechnology Information, The National Library of Medicine, The National Institutes of Health, Bethesda, MD 20894, USA.
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32
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Caetano-Anollés G, Nasir A, Kim KM, Caetano-Anollés D. Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions. Evol Bioinform Online 2018; 14:1176934318805101. [PMID: 30364468 PMCID: PMC6196624 DOI: 10.1177/1176934318805101] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/05/2018] [Indexed: 12/25/2022] Open
Abstract
Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the "tree of life," generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, Plön, Germany
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33
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Caetano-Anollés D, Caetano-Anollés K, Caetano-Anollés G. Evolution of macromolecular structure: a 'double tale' of biological accretion and diversification. Sci Prog 2018; 101:360-383. [PMID: 30296968 PMCID: PMC10365222 DOI: 10.3184/003685018x15379391431599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The evolution of structure in biology is driven by accretion and diversification. Accretion brings together disparate parts to form bigger wholes. Diversification provides opportunities for growth and innovation. Here, we review patterns and processes that are responsible for a 'double tale' of accretion and diversification at various levels of complexity, from proteins and nucleic acids to high-rise building structures in cities. Parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organise into modules with tight linkage. In a second phase, variants of the modules evolve and become new parts for a new generative cycle of higher-level organisation. Evolutionary genomics and network biology support the 'double tale' of structural module creation and validate an evolutionary principle of maximum abundance that drives the gain and loss of modules.
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Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics of the Max-Planck Institute for Evolutionary Biology, Plön, Germany. Developmental Biology from the University of Illinois, Urbana-Champaign
| | - Kelsey Caetano-Anollés
- Division of Biomedical Informatics of Seoul National University College of Medicine, Republic of Korea. Animal Sciences from the University of Illinois, Urbana-Champaign
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences and Affiliate of the C.R. Woese Institute for Genomic Biology at the University of Illinois, Urbana-Champaign. University of La Plata in Argentina
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34
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A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria. Antonie van Leeuwenhoek 2018; 112:101-107. [PMID: 30171432 DOI: 10.1007/s10482-018-1154-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/28/2018] [Indexed: 01/18/2023]
Abstract
Protein functional domains are semi-autonomous parts of proteins capable of functioning independently. One protein may contain several domains and one domain may be present in different protein sequences. Thus, protein domains represent the niche specific adaptive nature of an organism. We hypothesized that the presence and absence of protein domains in an organism could be used to make a phylogenetic tree, which may better depict the biotope (niche). Here, we selected 100 actinobacteria and built a phylogenetic tree depending upon the presence and absence of protein domains. Strains of different genera from the same niche were found to cluster together suggesting niche specific domain acquisition among selected strains. Thus, the domain based phylogeny clustered the selected actinobacteria mainly according to their niche rather than their taxonomic classification.
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35
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Nasir A, Kim KM, Caetano-Anollés G. Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells. Front Microbiol 2017; 8:1178. [PMID: 28690608 PMCID: PMC5481351 DOI: 10.3389/fmicb.2017.01178] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/09/2017] [Indexed: 01/05/2023] Open
Abstract
Untangling the origin and evolution of viruses remains a challenging proposition. We recently studied the global distribution of protein domain structures in thousands of completely sequenced viral and cellular proteomes with comparative genomics, phylogenomics, and multidimensional scaling methods. A tree of life describing the evolution of proteomes revealed viruses emerging from the base of the tree as a fourth supergroup of life. A tree of domains indicated an early origin of modern viral lineages from ancient cells that co-existed with the cellular ancestors. However, it was recently argued that the rooting of our trees and the basal placement of viruses was artifactually induced by small genome (proteome) size. Here we show that these claims arise from misunderstanding and misinterpretations of cladistic methodology. Trees are reconstructed unrooted, and thus, their topologies cannot be distorted a posteriori by the rooting methodology. Tracing proteome size in trees and multidimensional views of evolutionary relationships as well as tests of leaf stability and exclusion/inclusion of taxa demonstrated that the smallest proteomes were neither attracted toward the root nor caused any topological distortions of the trees. Simulations confirmed that taxa clustering patterns were independent of proteome size and were determined by the presence of known evolutionary relatives in data matrices, highlighting the need for broader taxon sampling in phylogeny reconstruction. Instead, phylogenetic tracings of proteome size revealed a slowdown in innovation of the structural domain vocabulary and four regimes of allometric scaling that reflected a Heaps law. These regimes explained increasing economies of scale in the evolutionary growth and accretion of kernel proteome repertoires of viruses and cellular organisms that resemble growth of human languages with limited vocabulary sizes. Results reconcile dynamic and static views of domain frequency distributions that are consistent with the axiom of spatiotemporal continuity that is tenet of evolutionary thinking.
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Affiliation(s)
- Arshan Nasir
- Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
| | - Kyung Mo Kim
- Division of Polar Life Sciences, Korea Polar Research InstituteIncheon, South Korea
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-ChampaignUrbana, IL, United States
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36
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Koç I, Caetano-Anollés G. The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data. PLoS One 2017; 12:e0176129. [PMID: 28467492 PMCID: PMC5414959 DOI: 10.1371/journal.pone.0176129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/05/2017] [Indexed: 11/18/2022] Open
Abstract
The origin and natural history of molecular functions hold the key to the emergence of cellular organization and modern biochemistry. Here we use a genomic census of Gene Ontology (GO) terms to reconstruct phylogenies at the three highest (1, 2 and 3) and the lowest (terminal) levels of the hierarchy of molecular functions, which reflect the broadest and the most specific GO definitions, respectively. These phylogenies define evolutionary timelines of functional innovation. We analyzed 249 free-living organisms comprising the three superkingdoms of life, Archaea, Bacteria, and Eukarya. Phylogenies indicate catalytic, binding and transport functions were the oldest, suggesting a 'metabolism-first' origin scenario for biochemistry. Metabolism made use of increasingly complicated organic chemistry. Primordial features of ancient molecular functions and functional recruitments were further distilled by studying the oldest child terms of the oldest level 1 GO definitions. Network analyses showed the existence of an hourglass pattern of enzyme recruitment in the molecular functions of the directed acyclic graph of molecular functions. Older high-level molecular functions were thoroughly recruited at younger lower levels, while very young high-level functions were used throughout the timeline. This pattern repeated in every one of the three mappings, which gave a criss-cross pattern. The timelines and their mappings were remarkable. They revealed the progressive evolutionary development of functional toolkits, starting with the early rise of metabolic activities, followed chronologically by the rise of macromolecular biosynthesis, the establishment of controlled interactions with the environment and self, adaptation to oxygen, and enzyme coordinated regulation, and ending with the rise of structural and cellular complexity. This historical account holds important clues for dissection of the emergence of biomcomplexity and life.
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Affiliation(s)
- Ibrahim Koç
- Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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Nasir A, Caetano-Anollés G. Identification of Capsid/Coat Related Protein Folds and Their Utility for Virus Classification. Front Microbiol 2017; 8:380. [PMID: 28344575 PMCID: PMC5344890 DOI: 10.3389/fmicb.2017.00380] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/23/2017] [Indexed: 12/31/2022] Open
Abstract
The viral supergroup includes the entire collection of known and unknown viruses that roam our planet and infect life forms. The supergroup is remarkably diverse both in its genetics and morphology and has historically remained difficult to study and classify. The accumulation of protein structure data in the past few years now provides an excellent opportunity to re-examine the classification and evolution of viruses. Here we scan completely sequenced viral proteomes from all genome types and identify protein folds involved in the formation of viral capsids and virion architectures. Viruses encoding similar capsid/coat related folds were pooled into lineages, after benchmarking against published literature. Remarkably, the in silico exercise reproduced all previously described members of known structure-based viral lineages, along with several proposals for new additions, suggesting it could be a useful supplement to experimental approaches and to aid qualitative assessment of viral diversity in metagenome samples.
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Affiliation(s)
- Arshan Nasir
- Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-ChampaignUrbana, IL, USA; Department of Biosciences, COMSATS Institute of Information TechnologyIslamabad, Pakistan
| | - Gustavo Caetano-Anollés
- Department of Crop Sciences, Evolutionary Bioinformatics Laboratory, University of Illinois at Urbana-Champaign Urbana, IL, USA
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Exploring the dark foldable proteome by considering hydrophobic amino acids topology. Sci Rep 2017; 7:41425. [PMID: 28134276 PMCID: PMC5278394 DOI: 10.1038/srep41425] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022] Open
Abstract
The protein universe corresponds to the set of all proteins found in all organisms. A way to explore it is by taking into account the domain content of the proteins. However, some part of sequences and many entire sequences remain un-annotated despite a converging number of domain families. The un-annotated part of the protein universe is referred to as the dark proteome and remains poorly characterized. In this study, we quantify the amount of foldable domains within the dark proteome by using the hydrophobic cluster analysis methodology. These un-annotated foldable domains were grouped using a combination of remote homology searches and domain annotations, leading to define different levels of darkness. The dark foldable domains were analyzed to understand what make them different from domains stored in databases and thus difficult to annotate. The un-annotated domains of the dark proteome universe display specific features relative to database domains: shorter length, non-canonical content and particular topology in hydrophobic residues, higher propensity for disorder, and a higher energy. These features make them hard to relate to known families. Based on these observations, we emphasize that domain annotation methodologies can still be improved to fully apprehend and decipher the molecular evolution of the protein universe.
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Caetano-Anollés D, Caetano-Anollés G. Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks. Life (Basel) 2016; 6:life6040043. [PMID: 27918435 PMCID: PMC5198078 DOI: 10.3390/life6040043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/21/2016] [Accepted: 11/29/2016] [Indexed: 01/10/2023] Open
Abstract
The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains. Here we review phylogenomic analyses that reconstruct the early history of the synthetase enzymes and the ribosome, their interactions with RNA, and the inception of amino acid charging and codon specificities in tRNA that are responsible for the genetic code. We also trace the age of domains and tRNA onto ancient tRNA homologies that were recently identified in rRNA. Our findings reveal a timeline of recruitment of tRNA building blocks for the formation of a functional ribosome, which holds both the biocatalytic functions of protein biosynthesis and the ability to store genetic memory in primordial RNA genomic templates.
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Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie, 24306 Plön, Germany.
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Abstract
Globular proteins typically fold into tightly packed arrays of regular secondary structures. We developed a model to approximate the compact parallel and antiparallel arrangement of α-helices and β-strands, enumerated all possible topologies formed by up to five secondary structural elements (SSEs), searched for their occurrence in spatial structures of proteins, and documented their frequencies of occurrence in the PDB. The enumeration model grows larger super-secondary structure patterns (SSPs) by combining pairs of smaller patterns, a process that approximates a potential path of protein fold evolution. The most prevalent SSPs are typically present in superfolds such as the Rossmann-like fold, the ferredoxin-like fold, and the Greek key motif, whereas the less frequent SSPs often possess uncommon structure features such as split β-sheets, left-handed connections, and crossing loops. This complete SSP enumeration model, for the first time, allows us to investigate which theoretically possible SSPs are not observed in available protein structures. All SSPs with up to four SSEs occurred in proteins. However, among the SSPs with five SSEs, approximately 20% (218) are absent from existing folds. Of these unobserved SSPs, 80% contain two or more uncommon structure features. To facilitate future efforts in protein structure classification, engineering, and design, we provide the resulting patterns and their frequency of occurrence in proteins at: http://prodata.swmed.edu/ssps/.
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Jelen BI, Giovannelli D, Falkowski PG. The Role of Microbial Electron Transfer in the Coevolution of the Biosphere and Geosphere. Annu Rev Microbiol 2016; 70:45-62. [PMID: 27297124 DOI: 10.1146/annurev-micro-102215-095521] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
All life on Earth is dependent on biologically mediated electron transfer (i.e., redox) reactions that are far from thermodynamic equilibrium. Biological redox reactions originally evolved in prokaryotes and ultimately, over the first ∼2.5 billion years of Earth's history, formed a global electronic circuit. To maintain the circuit on a global scale requires that oxidants and reductants be transported; the two major planetary wires that connect global metabolism are geophysical fluids-the atmosphere and the oceans. Because all organisms exchange gases with the environment, the evolution of redox reactions has been a major force in modifying the chemistry at Earth's surface. Here we briefly review the discovery and consequences of redox reactions in microbes with a specific focus on the coevolution of life and geochemical phenomena.
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Affiliation(s)
- Benjamin I Jelen
- Environmental Biophysics and Molecular Ecology Program, Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, New Jersey 08901; , ,
| | - Donato Giovannelli
- Environmental Biophysics and Molecular Ecology Program, Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, New Jersey 08901; , , .,Institute of Marine Science, National Research Council, 60125 Ancona, Italy.,Program in Interdisciplinary Studies, Institute for Advanced Studies, Princeton, New Jersey 08540.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan 152-8550
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Institute of Earth, Ocean and Atmospheric Sciences, Rutgers University, New Brunswick, New Jersey 08901; , , .,Department of Earth and Planetary Sciences, Rutgers University, New Brunswick, New Jersey 08854
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A Dynamic Model for the Evolution of Protein Structure. J Mol Evol 2016; 82:230-43. [PMID: 27146880 DOI: 10.1007/s00239-016-9740-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/12/2016] [Indexed: 10/21/2022]
Abstract
Domains are folded structures and evolutionary building blocks of protein molecules. Their three-dimensional atomic conformations, which define biological functions, can be coarse-grained into levels of a hierarchy. Here we build global dynamical models for the evolution of domains at fold and fold superfamily (FSF) levels. We fit the models with data from phylogenomic trees of domain structures and evaluate the distributions of the resulting parameters and their implications. The trees were inferred from a census of domain structures in hundreds of genomes from all three superkingdoms of life. The models used birth-death differential equations with the global abundances of structures as state variables, with one set of equations for folds and another for FSFs. Only the transitions present in the tree are assumed possible. Each fold or FSF diversifies in variants, eventually producing a new fold or FSF. The parameters specify rates of generation of variants and of new folds or FSFs. The equations were solved for the parameters by simplifying the trees to a comb-like topology, treating branches as emerging directly from a trunk. We found that the rate constants for folds and FSFs evolved similarly. These parameters showed a sharp transient change at about 1.5 Gyrs ago. This time coincides with a period in which domains massively combined in proteins and their arrangements distributed in novel lineages during the rise of organismal diversification. Our simulations suggest that exploration of protein structure space occurs through coarse-grained discoveries that undergo fine-grained elaboration.
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Xu J, Zhang J. Impact of structure space continuity on protein fold classification. Sci Rep 2016; 6:23263. [PMID: 27006112 PMCID: PMC4804218 DOI: 10.1038/srep23263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/03/2016] [Indexed: 11/09/2022] Open
Abstract
Protein structure classification hierarchically clusters domain structures based on structure and/or sequence similarities and plays important roles in the study of protein structure-function relationship and protein evolution. Among many classifications, SCOP and CATH are widely viewed as the gold standards. Fold classification is of special interest because this is the lowest level of classification that does not depend on protein sequence similarity. The current fold classifications such as those in SCOP and CATH are controversial because they implicitly assume that folds are discrete islands in the structure space, whereas increasing evidence suggests significant similarities among folds and supports a continuous fold space. Although this problem is widely recognized, its impact on fold classification has not been quantitatively evaluated. Here we develop a likelihood method to classify a domain into the existing folds of CATH or SCOP using both query-fold structure similarities and within-fold structure heterogeneities. The new classification differs from the original classification for 3.4-12% of domains, depending on factors such as the structure similarity score and original classification scheme used. Because these factors differ for different biological purposes, our results indicate that the importance of considering structure space continuity in fold classification depends on the specific question asked.
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Affiliation(s)
- Jinrui Xu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Brunk E, Mih N, Monk J, Zhang Z, O’Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO. Systems biology of the structural proteome. BMC SYSTEMS BIOLOGY 2016; 10:26. [PMID: 26969117 PMCID: PMC4787049 DOI: 10.1186/s12918-016-0271-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/16/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND The success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology. RESULTS Here, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository ( https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/). CONCLUSIONS Translating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM-PRO offers insight into the physical embodiment of an organism's genotype, and its use in this comparative framework enables exploration of adaptive strategies for these organisms, opening the door to many new lines of research. With these provided tools, tutorials, and background, the reader will be in a position to run GEM-PRO for their own purposes.
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Affiliation(s)
- Elizabeth Brunk
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
- />Joint BioEnergy Institute, Emeryville, CA 94608 USA
| | - Nathan Mih
- />Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA 92093 USA
| | - Jonathan Monk
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Zhen Zhang
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Edward J. O’Brien
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Spencer E. Bliven
- />Bioinformatics and Systems Biology Program, University of California, La Jolla, San Diego, CA 92093 USA
- />National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 USA
| | - Ke Chen
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
| | - Roger L. Chang
- />Department of Systems Biology, Harvard Medical School, Boston, MA 02115 USA
| | - Philip E. Bourne
- />Office of the Director, National Institutes of Health, Bethesda, MD 20894 USA
| | - Bernhard O. Palsson
- />Department of Bioengineering, University of California, La Jolla, San Diego, CA 92093 USA
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Kang SK, Chen BX, Tian T, Jia XS, Chu XY, Liu R, Dong PF, Yang QY, Zhang HY. ATP selection in a random peptide library consisting of prebiotic amino acids. Biochem Biophys Res Commun 2015; 466:400-5. [PMID: 26365351 DOI: 10.1016/j.bbrc.2015.09.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 09/08/2015] [Indexed: 01/02/2023]
Abstract
Based upon many theoretical findings on protein evolution, we proposed a ligand-selection model for the origin of proteins, in which the most ancient proteins originated from ATP selection in a pool of random peptides. To test this ligand-selection model, we constructed a random peptide library consisting of 15 types of prebiotic amino acids and then used cDNA display to perform six rounds of in vitro selection with ATP. By means of next-generation sequencing, the most prevalent sequence was defined. Biochemical and biophysical characterization of the selected peptide showed that it was stable and foldable and had ATP-hydrolysis activity as well.
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Affiliation(s)
- Shou-Kai Kang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Bai-Xue Chen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Tian Tian
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xi-Shuai Jia
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xin-Yi Chu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Rong Liu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Peng-Fei Dong
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qing-Yong Yang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Hong-Yu Zhang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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Caetano-Anollés G, Caetano-Anollés D. Computing the origin and evolution of the ribosome from its structure - Uncovering processes of macromolecular accretion benefiting synthetic biology. Comput Struct Biotechnol J 2015; 13:427-47. [PMID: 27096056 PMCID: PMC4823900 DOI: 10.1016/j.csbj.2015.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/16/2015] [Accepted: 07/19/2015] [Indexed: 12/11/2022] Open
Abstract
Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101W. Peabody Drive, Urbana, IL 61801, USA; C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Derek Caetano-Anollés
- C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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Caetano-Anollés G, Mittenthal JE, Caetano-Anollés D, Kim KM. A calibrated chronology of biochemistry reveals a stem line of descent responsible for planetary biodiversity. Front Genet 2014; 5:306. [PMID: 25309572 PMCID: PMC4161044 DOI: 10.3389/fgene.2014.00306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/18/2014] [Indexed: 11/13/2022] Open
Abstract
Time-calibrated phylogenomic trees of protein domain structure produce powerful chronologies describing the evolution of biochemistry and life. These timetrees are built from a genomic census of millions of encoded proteins using models of nested accumulation of molecules in evolving proteomes. Here we show that a primordial stem line of descent, a propagating series of pluripotent cellular entities, populates the deeper branches of the timetrees. The stem line produced for the first time cellular grades ~2.9 billion years (Gy)-ago, which slowly turned into lineages of superkingdom Archaea. Prompted by the rise of planetary oxygen and aerobic metabolism, the stem line also produced bacterial and eukaryal lineages. Superkingdom-specific domain repertoires emerged ~2.1 Gy-ago delimiting fully diversified Bacteria. Repertoires specific to Eukarya and Archaea appeared 300 millions years later. Results reconcile reductive evolutionary processes leading to the early emergence of Archaea to superkingdom-specific innovations compatible with a tree of life rooted in Bacteria.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana, IL, USA
| | - Jay E Mittenthal
- Department of Cell and Developmental Biology, University of Illinois Urbana, IL, USA
| | - Derek Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana, IL, USA
| | - Kyung Mo Kim
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology Daejeon, South Korea
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A phylogenomic census of molecular functions identifies modern thermophilic archaea as the most ancient form of cellular life. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:706468. [PMID: 25249790 PMCID: PMC4164138 DOI: 10.1155/2014/706468] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 11/20/2013] [Accepted: 01/17/2014] [Indexed: 12/30/2022]
Abstract
The origins of diversified life remain mysterious despite considerable efforts devoted to untangling the roots of the universal tree of life. Here we reconstructed phylogenies that described the evolution of molecular functions and the evolution of species directly from a genomic census of gene ontology (GO) definitions. We sampled 249 free-living genomes spanning organisms in the three superkingdoms of life, Archaea, Bacteria, and Eukarya, and used the abundance of GO terms as molecular characters to produce rooted phylogenetic trees. Results revealed an early thermophilic origin of Archaea that was followed by genome reduction events in microbial superkingdoms. Eukaryal genomes displayed extraordinary functional diversity and were enriched with hundreds of novel molecular activities not detected in the akaryotic microbial cells. Remarkably, the majority of these novel functions appeared quite late in evolution, synchronized with the diversification of the eukaryal superkingdom. The distribution of GO terms in superkingdoms confirms that Archaea appears to be the simplest and most ancient form of cellular life, while Eukarya is the most diverse and recent.
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Kim KM, Nasir A, Hwang K, Caetano-Anollés G. A tree of cellular life inferred from a genomic census of molecular functions. J Mol Evol 2014; 79:240-62. [PMID: 25128982 DOI: 10.1007/s00239-014-9637-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/05/2014] [Indexed: 10/24/2022]
Abstract
Phylogenomics aims to describe evolutionary relatedness between organisms by analyzing genomic data. The common practice is to produce phylogenomic trees from molecular information in the sequence, order, and content of genes in genomes. These phylogenies describe the evolution of life and become valuable tools for taxonomy. The recent availability of structural and functional data for hundreds of genomes now offers the opportunity to study evolution using more deep, conserved, and reliable sets of molecular features. Here, we reconstruct trees of life from the functions of proteins. We start by inferring rooted phylogenomic trees and networks of organisms directly from Gene Ontology annotations. Phylogenies and networks yield novel insights into the emergence and evolution of cellular life. The ancestor of Archaea originated earlier than the ancestors of Bacteria and Eukarya and was thermophilic. In contrast, basal bacterial lineages were non-thermophilic. A close relationship between Plants and Metazoa was also identified that disagrees with the traditional Fungi-Metazoa grouping. While measures of evolutionary reticulation were minimum in Eukarya and maximum in Bacteria, the massive role of horizontal gene transfer in microbes did not materialize in phylogenomic networks. Phylogenies and networks also showed that the best reconstructions were recovered when problematic taxa (i.e., parasitic/symbiotic organisms) and horizontally transferred characters were excluded from analysis. Our results indicate that functionomic data represent a useful addition to the set of molecular characters used for tree reconstruction and that trees of cellular life carry in deep branches considerable predictive power to explain the evolution of living organisms.
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Affiliation(s)
- Kyung Mo Kim
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea
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50
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Caetano-Anollés G, Nasir A, Zhou K, Caetano-Anollés D, Mittenthal JE, Sun FJ, Kim KM. Archaea: the first domain of diversified life. ARCHAEA (VANCOUVER, B.C.) 2014; 2014:590214. [PMID: 24987307 PMCID: PMC4060292 DOI: 10.1155/2014/590214] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 02/15/2014] [Accepted: 03/25/2014] [Indexed: 01/23/2023]
Abstract
The study of the origin of diversified life has been plagued by technical and conceptual difficulties, controversy, and apriorism. It is now popularly accepted that the universal tree of life is rooted in the akaryotes and that Archaea and Eukarya are sister groups to each other. However, evolutionary studies have overwhelmingly focused on nucleic acid and protein sequences, which partially fulfill only two of the three main steps of phylogenetic analysis, formulation of realistic evolutionary models, and optimization of tree reconstruction. In the absence of character polarization, that is, the ability to identify ancestral and derived character states, any statement about the rooting of the tree of life should be considered suspect. Here we show that macromolecular structure and a new phylogenetic framework of analysis that focuses on the parts of biological systems instead of the whole provide both deep and reliable phylogenetic signal and enable us to put forth hypotheses of origin. We review over a decade of phylogenomic studies, which mine information in a genomic census of millions of encoded proteins and RNAs. We show how the use of process models of molecular accumulation that comply with Weston's generality criterion supports a consistent phylogenomic scenario in which the origin of diversified life can be traced back to the early history of Archaea.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Arshan Nasir
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Kaiyue Zhou
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Derek Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jay E. Mittenthal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, Institute for Genomic Biology and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Feng-Jie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Kyung Mo Kim
- Microbial Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
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