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1. Reproductive Proteins Evolve Faster Than Non-reproductive Proteins Among Solanum Species

   https://doi.org/10.3389/fpls.2021.635990  

   Moyle, Leonie C.; Wu, Meng; Gibson, Matthew J. (April 2021, Frontiers in Plant Science)

   null (Ed.)

   Elevated rates of evolution in reproductive proteins are commonly observed in animal species, and are thought to be driven by the action of sexual selection and sexual conflict acting specifically on reproductive traits. Whether similar patterns are broadly observed in other biological groups is equivocal. Here, we examine patterns of protein divergence among wild tomato species ( Solanum section Lycopersicon ), to understand forces shaping the evolution of reproductive genes in this diverse, rapidly evolving plant clade. By comparing rates of molecular evolution among loci expressed in reproductive and non-reproductive tissues, our aims were to test if: (a) reproductive-specific loci evolve more rapidly, on average, than non-reproductive loci; (b) ‘male’-specific loci evolve at different rates than ‘female’-specific loci; (c) genes expressed exclusively in gametophytic (haploid) tissue evolve differently from genes expressed in sporophytic (diploid) tissue or in both tissue types; and (d) mating system variation (a potential proxy for the expected strength of sexual selection and/or sexual conflict) affects patterns of protein evolution. We observed elevated evolutionary rates in reproductive proteins. However, this pattern was most evident for female- rather than male-specific loci, both broadly and for individual loci inferred to be positively selected. These elevated rates might be facilitated by greater tissue-specificity of reproductive proteins, as faster rates were also associated with more narrow expression domains. In contrast, we found little evidence that evolutionary rates are consistently different in loci experiencing haploid selection (gametophytic-exclusive loci), or in lineages with quantitatively different mating systems. Overall while reproductive protein evolution is generally elevated in this diverse plant group, some specific patterns of evolution are more complex than those reported in other (largely animal) systems, and include a more prominent role for female-specific loci among adaptively evolving genes. 

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2. ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages

   https://doi.org/10.1093/pcp/pcad122  

   Waters, Elizabeth R.; Bezanilla, Magdalena; Vierling, Elizabeth (October 2023, Plant And Cell Physiology)

   Abstract ATPase family AAA domain–containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria. 

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3. Electron hopping through proteins

   https://doi.org/10.1016/j.ccr.2012.03.032  

   Warren, Jeffrey J.; Ener, Maraia E.; Vlček, Antonín; Winkler, Jay R.; Gray, Harry B. (November 2012, Coordination Chemistry Reviews)
4. Theta‐curves in proteins

   https://doi.org/10.1002/pro.5133  

   Dabrowski‐Tumanski, Pawel; Goundaroulis, Dimos; Stasiak, Andrzej; Rawdon, Eric_J; Sulkowska, Joanna_I (August 2024, Protein Science)

   Abstract We study and characterize the topology of connectivity circuits observed in natively folded protein structures whose coordinates are deposited in the Protein Data Bank (PDB). Polypeptide chains of some proteins naturally fold into unique knotted configurations. Another kind of nontrivial topology of polypeptide chains is observed when, in addition to covalent bonds connecting consecutive amino acids in polypeptide chains, one also considers disulfide and ionic bonds between non‐consecutive amino acids. Bonds between non‐consecutive amino acids introduce bifurcation points into connectivity circuits defined by bonds between consecutive and nonconsecutive amino acids in analyzed proteins. Circuits with bifurcation points can form θ‐curves with various topologies. We catalog here the observed topologies of θ‐curves passing through bridges between consecutive and non‐consecutive amino acids in studied proteins. 

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5. Direct Cytosolic Delivery of Proteins through Coengineering of Proteins and Polymeric Delivery Vehicles

   https://doi.org/10.1021/jacs.9b12759  

   Lee, Yi-Wei; Luther, David C.; Goswami, Ritabrita; Jeon, Taewon; Clark, Vincent; Elia, James; Gopalakrishnan, Sanjana; Rotello, Vincent M. (March 2020, Journal of the American Chemical Society)