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Velle KB, Swafford AJM, Garner E, Fritz-Laylin LK. Actin network evolution as a key driver of eukaryotic diversification. J Cell Sci 2024; 137:jcs261660. [PMID: 39120594 DOI: 10.1242/jcs.261660] [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: 08/10/2024] Open
Abstract
Eukaryotic cells have been evolving for billions of years, giving rise to wildly diverse cell forms and functions. Despite their variability, all eukaryotic cells share key hallmarks, including membrane-bound organelles, heavily regulated cytoskeletal networks and complex signaling cascades. Because the actin cytoskeleton interfaces with each of these features, understanding how it evolved and diversified across eukaryotic phyla is essential to understanding the evolution and diversification of eukaryotic cells themselves. Here, we discuss what we know about the origin and diversity of actin networks in terms of their compositions, structures and regulation, and how actin evolution contributes to the diversity of eukaryotic form and function.
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Affiliation(s)
- Katrina B Velle
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | | | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024; 25:416-430. [PMID: 38263430 DOI: 10.1038/s41576-023-00688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/25/2024]
Abstract
Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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Zheng J, Mallon J, Lammers A, Rados T, Litschel T, Moody ERR, Ramirez-Diaz DA, Schmid A, Williams TA, Bisson-Filho AW, Garner E. Salactin, a dynamically unstable actin homolog in Haloarchaea. mBio 2023; 14:e0227223. [PMID: 37966230 PMCID: PMC10746226 DOI: 10.1128/mbio.02272-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE Protein filaments play important roles in many biological processes. We discovered an actin homolog in halophilic archaea, which we call Salactin. Just like the filaments that segregate DNA in eukaryotes, Salactin grows out of the cell poles towards the middle, and then quickly depolymerizes, a behavior known as dynamic instability. Furthermore, we see that Salactin affects the distribution of DNA in daughter cells when cells are grown in low-phosphate media, suggesting Salactin filaments might be involved in segregating DNA when the cell has only a few copies of the chromosome.
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Affiliation(s)
- Jenny Zheng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - John Mallon
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Alex Lammers
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- Department of Biomedical Engineering, The Biological Design Center, Boston University, Boston, Massachusetts, USA
- The Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Theopi Rados
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Thomas Litschel
- Physiology Course, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA
| | - Edmund R. R. Moody
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
| | - Diego A. Ramirez-Diaz
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amy Schmid
- Department of Biology, Duke University, Durham, North Carolina, USA
- Center for Genomics and Computational Biology, Duke University, Durham, North Carolina, USA
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexandre W. Bisson-Filho
- Department of Biology, Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, USA
| | - Ethan Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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Cyanobacterial membrane dynamics in the light of eukaryotic principles. Biosci Rep 2023; 43:232406. [PMID: 36602300 PMCID: PMC9950537 DOI: 10.1042/bsr20221269] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Intracellular compartmentalization is a hallmark of eukaryotic cells. Dynamic membrane remodeling, involving membrane fission/fusion events, clearly is crucial for cell viability and function, as well as membrane stabilization and/or repair, e.g., during or after injury. In recent decades, several proteins involved in membrane stabilization and/or dynamic membrane remodeling have been identified and described in eukaryotes. Yet, while typically not having a cellular organization as complex as eukaryotes, also bacteria can contain extra internal membrane systems besides the cytoplasmic membranes (CMs). Thus, also in bacteria mechanisms must have evolved to stabilize membranes and/or trigger dynamic membrane remodeling processes. In fact, in recent years proteins, which were initially defined being eukaryotic inventions, have been recognized also in bacteria, and likely these proteins shape membranes also in these organisms. One example of a complex prokaryotic inner membrane system is the thylakoid membrane (TM) of cyanobacteria, which contains the complexes of the photosynthesis light reaction. Cyanobacteria are evolutionary closely related to chloroplasts, and extensive remodeling of the internal membrane systems has been observed in chloroplasts and cyanobacteria during membrane biogenesis and/or at changing light conditions. We here discuss common principles guiding eukaryotic and prokaryotic membrane dynamics and the proteins involved, with a special focus on the dynamics of the cyanobacterial TMs and CMs.
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Ponlachantra K, Suginta W, Robinson RC, Kitaoku Y. AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea. Bioessays 2023; 45:e2200119. [PMID: 36461738 DOI: 10.1002/bies.202200119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.
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Affiliation(s)
- Khongpon Ponlachantra
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.,Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
| | - Yoshihito Kitaoku
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
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