Convergent evolution of the Hedgehog/Intein fold in protein splicing

AbstractThe widely used molecular evolutionary clock assumes the divergent evolution of proteins. Convergent evolution has been proposed only for small protein elements but not for an entire protein fold. We investigated the structural basis of the protein splicing mechanism by class 3 inteins, which is distinct from class 1 and 2 inteins. We gathered structural and mechanistic evidence supporting the notion that the Hedgehog/INTein (HINT) superfamily fold, commonly found in protein splicing and related phenomena, could be an example of convergent evolution of an entire protein fold. We propose that the HINT fold is a structural and biochemical solution for trans-peptidyl and trans-esterification reactions.

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The Convergence of the Hedgehog/Intein Fold in Different Protein Splicing Mechanisms

International Journal of Molecular Sciences ◽

10.3390/ijms21218367 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8367

Author(s):

Hannes M. Beyer ◽

Salla I. Virtanen ◽

A. Sesilja Aranko ◽

Kornelia M. Mikula ◽

George T. Lountos ◽

...

Keyword(s):

Amino Acid ◽

Active Sites ◽

Bond Cleavage ◽

Structural Basis ◽

Protein Splicing ◽

Active Site Residues ◽

Class 1 ◽

Characteristic Sequences ◽

Dynamics Simulations ◽

Esterification Reactions

Protein splicing catalyzed by inteins utilizes many different combinations of amino-acid types at active sites. Inteins have been classified into three classes based on their characteristic sequences. We investigated the structural basis of the protein splicing mechanism of class 3 inteins by determining crystal structures of variants of a class 3 intein from Mycobacterium chimaera and molecular dynamics simulations, which suggested that the class 3 intein utilizes a different splicing mechanism from that of class 1 and 2 inteins. The class 3 intein uses a bond cleavage strategy reminiscent of proteases but share the same Hedgehog/INTein (HINT) fold of other intein classes. Engineering of class 3 inteins from a class 1 intein indicated that a class 3 intein would unlikely evolve directly from a class 1 or 2 intein. The HINT fold appears as structural and functional solution for trans-peptidyl and trans-esterification reactions commonly exploited by diverse mechanisms using different combinations of amino-acid types for the active-site residues.

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Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1920097117 ◽

2020 ◽

Vol 117 (20) ◽

pp. 10806-10817 ◽

Cited By ~ 6

Author(s):

Michael P. Torrens-Spence ◽

Ying-Chih Chiang ◽

Tyler Smith ◽

Maria A. Vicent ◽

Yi Wang ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Convergent Evolution ◽

Structural Features ◽

Divergent Evolution ◽

Structural Basis ◽

Acid Decarboxylase ◽

Substrate Selectivity ◽

Amino Acid Decarboxylase ◽

Catalytic Mechanisms

Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

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SARS-CoV-2 RBD in vitro evolution parrots and predicts contagious mutation spread

10.21203/rs.3.rs-183310/v1 ◽

2021 ◽

Author(s):

Gideon Schreiber ◽

Jiri Zahradník ◽

Shir Marciano ◽

Maya Shemesh ◽

Eyal Zoler ◽

...

Keyword(s):

South African ◽

Convergent Evolution ◽

Vaccine Development ◽

Spike Protein ◽

Structural Basis ◽

Receptor Binding Domain ◽

In Vitro Evolution ◽

High Affinity ◽

Future Drug

Abstract SARS-CoV-2 is continually evolving, with more contagious mutations spreading rapidly. Using in vitro evolution to affinity maturate the receptor-binding domain (RBD) of the spike protein towards ACE2 resulted in the more contagious mutations, S477N, E484K, and N501Y, to be among the first selected, explaining the convergent evolution of the “European” (20E-EU1), “British” (501.V1),”South African” (501.V2), and Brazilian variants (501.V3). Plotting the binding affinity to ACE2 of all RBD mutations against their incidence in the population shows a strong correlation between the two. Further in vitro evolution enhancing binding by 600-fold provides guidelines towards potentially new evolving mutations with even higher infectivity. For example, Q498R epistatic to N501Y. Nevertheless, the high-affinity RBD is also an efficient drug, inhibiting SARS-CoV-2 infection. The 2.9Å Cryo-EM structure of the high-affinity complex, including all rapidly spreading mutations, provides a structural basis for future drug and vaccine development and for in silico evaluation of known antibodies.

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Enzyme discovery beyond homology: a unique hydroxynitrile lyase in the Bet v1 superfamily

Scientific Reports ◽

10.1038/srep46738 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 9

Author(s):

Elisa Lanfranchi ◽

Tea Pavkov-Keller ◽

Eva-Maria Koehler ◽

Matthias Diepold ◽

Kerstin Steiner ◽

...

Keyword(s):

Convergent Evolution ◽

Stereoselective Synthesis ◽

Protein Crystallography ◽

Biochemical Properties ◽

Omics Data ◽

Protein Fold ◽

Hydroxynitrile Lyase ◽

Catalytic Center ◽

Enzyme Discovery ◽

Bet V1

Abstract Homology and similarity based approaches are most widely used for the identification of new enzymes for biocatalysis. However, they are not suitable to find truly novel scaffolds with a desired function and this averts options and diversity. Hydroxynitrile lyases (HNLs) are an example of non-homologous isofunctional enzymes for the synthesis of chiral cyanohydrins. Due to their convergent evolution, finding new representatives is challenging. Here we show the discovery of unique HNL enzymes from the fern Davallia tyermannii by coalescence of transcriptomics, proteomics and enzymatic screening. It is the first protein with a Bet v1-like protein fold exhibiting HNL activity, and has a new catalytic center, as shown by protein crystallography. Biochemical properties of D. tyermannii HNLs open perspectives for the development of a complementary class of biocatalysts for the stereoselective synthesis of cyanohydrins. This work shows that systematic integration of -omics data facilitates discovery of enzymes with unpredictable sequences and helps to extend our knowledge about enzyme diversity.

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Silent nucleotide substitutions and the molecular evolutionary clock

Science ◽

10.1126/science.7434017 ◽

1980 ◽

Vol 210 (4473) ◽

pp. 973-978 ◽

Cited By ~ 55

Author(s):

T. Jukes

Keyword(s):

Nucleotide Substitutions ◽

Molecular Evolutionary Clock ◽

Evolutionary Clock

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Transitions, transversions, and the molecular evolutionary clock

Journal of Molecular Evolution ◽

10.1007/bf02111284 ◽

1987 ◽

Vol 26 (1-2) ◽

pp. 87-98 ◽

Cited By ~ 17

Author(s):

Thomas H. Jukes

Keyword(s):

Molecular Evolutionary Clock ◽

Evolutionary Clock

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The Study of Plant Phylogeny Using Amino-Acid-Sequences of Ribulose-1,5-Bisphosphate Carboxylase .VI. Some Solanum and Allied Species From Different Continents

Australian Journal of Botany ◽

10.1071/bt9860187 ◽

1986 ◽

Vol 34 (2) ◽

pp. 187 ◽

Cited By ~ 5

Author(s):

PG Martin ◽

JM Dowd ◽

C Morris ◽

DE Symon

Keyword(s):

Amino Acid ◽

Continental Drift ◽

Small Subunit ◽

Amino Acid Sequences ◽

Ribulose Bisphosphate Carboxylase ◽

Ribulose Bisphosphate ◽

Bisphosphate Carboxylase ◽

Plant Phylogeny ◽

Molecular Evolutionary Clock ◽

Evolutionary Clock

The N-terminal 40 amino acid sequences of the small subunit of ribulose bisphosphate carboxylase have been determined for 13 species of Solanum, one other species of Solanaceae and two of Convolvulaceae. From these, and previously published sequences from Solanaceae, a minimal phylogenetic tree is derived. This agrees well with current taxonomy; the first dichotomy in the Solanaceae tree is between the two subfamilies Solanoideae and Cestroideae; within Solanum the subgenera Solanum and Leptostemonum separate dichotomously; within subgenus Leptostemonum the African and Asian species diverge from the Australian. Within the Australian species of subgenus Leptostemonum two most unusual substitutions have been noted. The implications for the hypotheses of a 'molecular evolutionary clock' and of biogeographical dispersal by continental drift are discussed.

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Hearing with the mouthparts: behavioural responses and the structural basis of ultrasound perception in acherontiine hawkmoths

Journal of Experimental Biology ◽

10.1242/jeb.202.8.909 ◽

1999 ◽

Vol 202 (8) ◽

pp. 909-918 ◽

Cited By ~ 1

Author(s):

M.C. Gopfert ◽

L.T. Wasserthal

Keyword(s):

Convergent Evolution ◽

Sensory Organ ◽

Structural Basis ◽

Flight Pattern ◽

Behavioural Responses ◽

Tethered Flight ◽

Hearing Organ ◽

Structural Differences ◽

Auditory Functions ◽

Species Specific

In contrast to previous assumptions, mouthparts form hearing organs not only in choerocampine hawkmoths but also in some distantly related acherontiine hawkmoth species. Four of the six acherontiine species studied revealed responses to ultrasonic sounds when stimulated during tethered flight. The responses included changes in flight speed and non-directional turns. Individuals from two species also responded by emitting sound. The minimum thresholds of the flight pattern changes were approximately 70 dB in all species studied, with species-specific best frequencies between 30 and 70 kHz. Some acherontiine species also move their tongue in a stereotyped way when stimulated acoustically. The activity of the muscles involved in this tongue reflex was characterized in the present study and used in combination with ablation experiments to localize the hearing organ. These experiments revealed auditory functions of the labial palps and the labral pilifers similar to those found in Choerocampina. The palp contributes a 20–25 dB rise in sensitivity, whereas the pilifer appears to contain the sensory organ. Structural differences suggest a convergent evolution of hearing in hawkmoths: in the place of the swollen palps of Choerocampina, acherontiine species capable of hearing possess a scale-plate of the palps that interacts with an articulating pilifer, while this modification is absent in closely related non-hearing species.

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