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Different protein sequences can give rise to highly similar folds through different stabilizing interactions.

ABSTRACT: We report an interesting case of structural similarity between 2 small, nonhomologous proteins, the third domain of ovomucoid (ovomucoid) and the C-terminal fragment of ribosomal L7/L12 protein (CTF). The region of similarity consists of a 3-stranded beta-sheet and an alpha-helix. This region is highly similar; the corresponding elements of secondary structure share a common topology, and the RMS difference for "equivalent" C alpha atoms is 1.6 A. Surprisingly, this common structure arises from completely different sequences. For the common core, the sequence identity is less than 3%, and there is neither significant sequence similarity nor similarity in the position or orientation of conserved hydrophobic residues. This superposition raises the question of how 2 entirely different sequences can produce an identical structure. Analyzing this common region in ovomucoid revealed that it is stabilized by disulfide bonds. In contrast, the corresponding structure in CTF is stabilized in the alpha-helix by a composition of residues with high helix-forming propensities. This result suggests that different sequences and different stabilizing interactions can produce an identical structure.

SUBMITTER: Laurents DV

PROVIDER: S-EPMC2142644 | biostudies-other | 1994 Nov

REPOSITORIES: biostudies-other

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Different protein sequences can give rise to highly similar folds through different stabilizing interactions.

Laurents D V DV Subbiah S S Levitt M M

Protein science : a publication of the Protein Society 19941101 11

We report an interesting case of structural similarity between 2 small, nonhomologous proteins, the third domain of ovomucoid (ovomucoid) and the C-terminal fragment of ribosomal L7/L12 protein (CTF). The region of similarity consists of a 3-stranded beta-sheet and an alpha-helix. This region is highly similar; the corresponding elements of secondary structure share a common topology, and the RMS difference for "equivalent" C alpha atoms is 1.6 A. Surprisingly, this common structure arises from ...[more]

PMID: 7703840

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Project description:Microbiomes often benefit plants, conferring resistance to pathogens, improving stress tolerance, or promoting plant growth. As potential plant mutualists, however, microbiomes are not a single organism but a community of species with complex interactions among microbial taxa and between microbes and their shared host. The nature of ecological interactions among microbes in the microbiome can have important consequences for the net effects of microbiomes on hosts. Here, we compared the effects of individual microbial strains and 10-strain synthetic communities on microbial productivity and host growth using the common duckweed Lemna minor and a synthetic, simplified version of its native microbiome. Except for Pseudomonas protegens, which was a mutualist when tested alone, all of the single strains we tested were commensals on hosts, benefiting from plant presence but not increasing host growth relative to uninoculated controls. However, 10-strain synthetic microbial communities increased both microbial productivity and duckweed growth more than the average single-strain inoculation and uninoculated controls, meaning that host-microbiome mutualisms can emerge from community interactions among microbes on hosts. The effects of community inoculation were sub-additive, suggesting at least some competition among microbes in the duckweed microbiome. We also investigated the relationship between L. minor fitness and that of its microbes, providing some of the first empirical estimates of broad fitness alignment between plants and members of their microbiomes; hosts grew faster with more productive microbes or microbiomes.ImportanceThere is currently substantial interest in engineering synthetic microbiomes for health or agricultural applications. One key question is how multi-strain microbial communities differ from single microbial strains in their productivity and effects on hosts. We tested 20 single bacterial strains and 2 distinct 10-strain synthetic communities on plant hosts and found that 10-strain communities led to faster host growth and greater microbial productivity than the average, but not the best, single strain. Furthermore, the microbial strains or communities that achieved the greatest cell densities were also the most beneficial to their hosts, showing that both specific single strains and multi-strain synthetic communities can engage in high-quality mutualisms with their hosts. Our results suggest that ~5% of single strains, as well as multi-strain synthetic communities comprised largely of commensal microbes, can benefit hosts and result in effective host-microbe mutualisms.

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Different protein sequences can give rise to highly similar folds through different stabilizing interactions.

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Different protein sequences can give rise to highly similar folds through different stabilizing interactions.

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