Dataset Information

Urm1: A Non-Canonical UBL.

ABSTRACT: Urm1 (ubiquitin related modifier 1) is a molecular fossil in the class of ubiquitin-like proteins (UBLs). It encompasses characteristics of classical UBLs, such as ubiquitin or SUMO (small ubiquitin-related modifier), but also of bacterial sulfur-carrier proteins (SCP). Since its main function is to modify tRNA, Urm1 acts in a non-canonical manner. Uba4, the activating enzyme of Urm1, contains two domains: a classical E1-like domain (AD), which activates Urm1, and a rhodanese homology domain (RHD). This sulfurtransferase domain catalyzes the formation of a C-terminal thiocarboxylate on Urm1. Thiocarboxylated Urm1 is the sulfur donor for 5-methoxycarbonylmethyl-2-thiouridine (mcm⁵s²U), a chemical nucleotide modification at the wobble position in tRNA. This thio-modification is conserved in all domains of life and optimizes translation. The absence of Urm1 increases stress sensitivity in yeast triggered by defects in protein homeostasis, a hallmark of neurological defects in higher organisms. In contrast, elevated levels of tRNA modifying enzymes promote the appearance of certain types of cancer and the formation of metastasis. Here, we summarize recent findings on the unique features that place Urm1 at the intersection of UBL and SCP and make Urm1 an excellent model for studying the evolution of protein conjugation and sulfur-carrier systems.

SUBMITTER: Termathe M

PROVIDER: S-EPMC7911844 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Urm1: A Non-Canonical UBL.

Termathe Martin M Leidel Sebastian A SA

Biomolecules 20210122 2

Urm1 (ubiquitin related modifier 1) is a molecular fossil in the class of ubiquitin-like proteins (UBLs). It encompasses characteristics of classical UBLs, such as ubiquitin or SUMO (small ubiquitin-related modifier), but also of bacterial sulfur-carrier proteins (SCP). Since its main function is to modify tRNA, Urm1 acts in a non-canonical manner. Uba4, the activating enzyme of Urm1, contains two domains: a classical E1-like domain (AD), which activates Urm1, and a rhodanese homology domain (RH ...[more]

PMID: 33499055

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Project description:This study investigates global properties of three categories of English text: canonical fiction, non-canonical fiction, and non-fictional texts. The central hypothesis of the study is that there are systematic differences with respect to structural design features between canonical and non-canonical fiction, and between fictional and non-fictional texts. To investigate these differences, we compiled a corpus containing texts of the three categories of interest, the Jena Corpus of Expository and Fictional Prose (JEFP Corpus). Two aspects of global structure are investigated, variability and self-similar (fractal) patterns, which reflect long-range correlations along texts. We use four types of basic observations, (i) the frequency of POS-tags per sentence, (ii) sentence length, (iii) lexical diversity, and (iv) the distribution of topic probabilities in segments of texts. These basic observations are grouped into two more general categories, (a) the lower-level properties (i) and (ii), which are observed at the level of the sentence (reflecting linguistic decoding), and (b) the higher-level properties (iii) and (iv), which are observed at the textual level (reflecting comprehension/integration). The observations for each property are transformed into series, which are analyzed in terms of variance and subjected to Multi-Fractal Detrended Fluctuation Analysis (MFDFA), giving rise to three statistics: (i) the degree of fractality ( H ), (ii) the degree of multifractality ( D ), i.e., the width of the fractal spectrum, and (iii) the degree of asymmetry ( A ) of the fractal spectrum. The statistics thus obtained are compared individually across text categories and jointly fed into a classification model (Support Vector Machine). Our results show that there are in fact differences between the three text categories of interest. In general, lower-level text properties are better discriminators than higher-level text properties. Canonical fictional texts differ from non-canonical ones primarily in terms of variability in lower-level text properties. Fractality seems to be a universal feature of text, slightly more pronounced in non-fictional than in fictional texts. On the basis of our results obtained on the basis of corpus data we point out some avenues for future research leading toward a more comprehensive analysis of textual aesthetics, e.g., using experimental methodologies.

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Urm1: A Non-Canonical UBL.

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Urm1: A Non-Canonical UBL.

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