scholarly journals Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function

2016 ◽  
Vol 216 (2) ◽  
pp. 605-616 ◽  
Author(s):  
David M. Goad ◽  
Chuanmei Zhu ◽  
Elizabeth A. Kellogg
Keyword(s):  
Shared Function

scholarly journals Analysis of thepdx-1(snz-1/sno-1) Region of theNeurospora crassaGenome: Correlation of Pyridoxine-Requiring Phenotypes With Mutations in Two Structural Genes

Genetics ◽  
2001 ◽  
Vol 157 (3) ◽  
pp. 1067-1075 ◽  
Author(s):  
Laura E Bean ◽  
William H Dvorachek ◽  
Edward L Braun ◽  
Allison Errett ◽  
Gregory S Saenz ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Stationary Phase ◽  
Neurospora Crassa ◽  
Vitamin B6 ◽  
Structural Genes ◽  
Protein Coding ◽  
Previous Conclusion ◽  
Protein Coding Genes ◽  
Shared Function ◽  
High Gene

AbstractWe report the analysis of a 36-kbp region of the Neurospora crassa genome, which contains homologs of two closely linked stationary phase genes, SNZ1 and SNO1, from Saccharomyces cerevisiae. Homologs of SNZ1 encode extremely highly conserved proteins that have been implicated in pyridoxine (vitamin B6) metabolism in the filamentous fungi Cercospora nicotianae and in Aspergillus nidulans. In N. crassa, SNZ and SNO homologs map to the region occupied by pdx-1 (pyridoxine requiring), a gene that has been known for several decades, but which was not sequenced previously. In this study, pyridoxine-requiring mutants of N. crassa were found to possess mutations that disrupt conserved regions in either the SNZ or SNO homolog. Previously, nearly all of these mutants were classified as pdx-1. However, one mutant with a disrupted SNO homolog was at one time designated pdx-2. It now appears appropriate to reserve the pdx-1 designation for the N. crassa SNZ homolog and pdx-2 for the SNO homolog. We further report annotation of the entire 36,030-bp region, which contains at least 12 protein coding genes, supporting a previous conclusion of high gene densities (12,000-13,000 total genes) for N. crassa. Among genes in this region other than SNZ and SNO homologs, there was no evidence of shared function. Four of the genes in this region appear to have been lost from the S. cerevisiae lineage.

scholarly journals Axes of inter-sample variability among transcriptional neighborhoods reveal disease associated cell states in single-cell data

2021 ◽  
Author(s):  
Yakir A Reshef ◽  
Laurie Rumker ◽  
Joyce B Kang ◽  
Aparna Nathan ◽  
Megan B Murray ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Single Cell ◽  
Active Tuberculosis ◽  
Cell Populations ◽  
Cell Type ◽  
Accurate Identification ◽  
Shared Function ◽  
Statistical Approaches ◽  
Cell Data ◽  
Notch Activation

As single-cell datasets grow in sample size, there is a critical need to characterize cell states that vary across samples and associate with sample attributes like clinical phenotypes. Current statistical approaches typically map cells to cell-type clusters and examine sample differences through that lens alone. Here we present covarying neighborhood analysis (CNA), an unbiased method to identify cell populations of interest with greater flexibility and granularity. CNA characterizes dominant axes of variation across samples by identifying groups of very small regions in transcriptional space, termed neighborhoods, that covary in abundance across samples, suggesting shared function or regulation. CNA can then rigorously test for associations between any sample-level attribute and the abundances of these covarying neighborhood groups. We show in simulation that CNA enables more powerful and accurate identification of disease-associated cell states than a cluster-based approach. When applied to published datasets, CNA captures a Notch activation signature in rheumatoid arthritis, redefines monocyte populations expanded in sepsis, and identifies a previously undiscovered T-cell population associated with progression to active tuberculosis.

scholarly journals FXYD3 (Mat-8), a New Regulator of Na,K-ATPase

2005 ◽  
Vol 16 (5) ◽  
pp. 2363-2371 ◽  
Author(s):  
Gilles Crambert ◽  
Ciming Li ◽  
Dirk Claeys ◽  
Käthi Geering
Keyword(s):  
Membrane Proteins ◽  
Transport Properties ◽  
Signal Peptide ◽  
Xenopus Oocytes ◽  
Type I ◽  
Mucous Cells ◽  
Β Subunit ◽  
Apparent Affinity ◽  
Shared Function

Four of the seven members of the FXYD protein family have been identified as specific regulators of Na,K-ATPase. In this study, we show that FXYD3, also known as Mat-8, is able to associate with and to modify the transport properties of Na,K-ATPase. In addition to this shared function, FXYD3 displays some uncommon characteristics. First, in contrast to other FXYD proteins, which were shown to be type I membrane proteins, FXYD3 may have a second transmembrane-like domain because of the presence of a noncleavable signal peptide. Second, FXYD3 can associate with Na,K- as well as H,K-ATPases when expressed in Xenopus oocytes. However, in situ (stomach), FXYD3 is associated only with Na,K-ATPase because its expression is restricted to mucous cells in which H,K-ATPase is absent. Coexpressed in Xenopus oocytes, FXYD3 modulates the glycosylation processing of the β subunit of X,K-ATPase dependent on the presence of the signal peptide. Finally, FXYD3 decreases both the apparent affinity for Na+ and K+ of Na,K-ATPase.

Shared function and moonlighting proteins in molybdenum cofactor biosynthesis

2017 ◽  
Vol 398 (9) ◽  
pp. 1009-1026 ◽  
Author(s):  
Silke Leimkühler
Keyword(s):  
Catalytic Reaction ◽  
Molybdenum Cofactor ◽  
Molybdenum Atom ◽  
Cluster Assembly ◽  
Shared Function ◽  
Cofactor Biosynthesis ◽  
Moonlighting Proteins ◽  
Cellular Pathways ◽  
Molybdenum Cofactor Biosynthesis ◽  
Protein Components

Abstract The biosynthesis of the molybdenum cofactor (Moco) is a highly conserved pathway in bacteria, archaea and eukaryotes. The molybdenum atom in Moco-containing enzymes is coordinated to the dithiolene group of a tricyclic pyranopterin monophosphate cofactor. The biosynthesis of Moco can be divided into three conserved steps, with a fourth present only in bacteria and archaea: (1) formation of cyclic pyranopterin monophosphate, (2) formation of molybdopterin (MPT), (3) insertion of molybdenum into MPT to form Mo-MPT, and (4) additional modification of Mo-MPT in bacteria with the attachment of a GMP or CMP nucleotide, forming the dinucleotide variants of Moco. While the proteins involved in the catalytic reaction of each step of Moco biosynthesis are highly conserved among the Phyla, a surprising link to other cellular pathways has been identified by recent discoveries. In particular, the pathways for FeS cluster assembly and thio-modifications of tRNA are connected to Moco biosynthesis by sharing the same protein components. Further, proteins involved in Moco biosynthesis are not only shared with other pathways, but additionally have moonlighting roles. This review gives an overview of Moco biosynthesis in bacteria and humans and highlights the shared function and moonlighting roles of the participating proteins.

diversity of Maa (Nilotic) adverbs

2020 ◽  
Vol 49 (2) ◽  
Author(s):  
Doris Payne
Keyword(s):  
Relative Clauses ◽  
Single Class ◽  
Prepositional Phrases ◽  
Nominal Phrase ◽  
Wide Range ◽  
Shared Function ◽  
Word Classes ◽  
Aspect Markers ◽  
Historical Origins ◽  
Relational Nouns

Maa linguistic varieties (Maasai, Parakuyo, Chamus, Samburu, among others), of the Eastern Nilotic family (Nilo-Saharan phylum), have words which can modify a predicate or predication and have the function of what cross-linguistically are called adverbs. While these words can be considered a single class due to this shared function and distribution, there are nevertheless morphosyntactic and usage distinctions. This is partly due to disparate historical origins, but also to semantics and different typical collocations. Among other distinctions, some adverbs can function as nominal tense/aspect markers within a determined nominal phrase (DP). Though the origins of all adverbs cannot be traced, the paper documents sources in oblique prepositional phrases, relational nouns, adjectives, relative clauses, and perhaps infinitive verbs, involving a wide range of lexical roots, such as ‘little’, ‘paint, mark’, ‘be abundant (with grass), be generous’, and others. Some synchronic adverbs do not have evident sources in other word classes, including the ­most frequently used word for ‘previously, before’, and the modal adverb ‘probably not, unlikely’ which is also an attenuative adverb. Maa adjectives and nouns largely overlap in their morphosyntax, but the ability to be modified by certain adverbs distinguishes them.

scholarly journals Meis family proteins are required for hindbrain development in the zebrafish

Development ◽  
2002 ◽  
Vol 129 (3) ◽  
pp. 585-595 ◽  
Author(s):  
Seong-Kyu Choe ◽  
Nikolaos Vlachakis ◽  
Charles G. Sagerström
Keyword(s):  
Gene Expression ◽  
Specific Gene ◽  
Homeodomain Proteins ◽  
Hox Proteins ◽  
Conserved Domain ◽  
Shared Function ◽  
Development And Differentiation ◽  
Transcription Complexes ◽  
Hox Cofactors

Meis homeodomain proteins function as Hox-cofactors by binding Pbx and Hox proteins to form multimeric complexes that control transcription of genes involved in development and differentiation. It is not known what role Meis proteins play in these complexes, nor is it clear which Hox functions require Meis proteins in vivo. We now show that a divergent Meis family member, Prep1, acts as a Hox co-factor in zebrafish. This suggests that all Meis family members have at least one shared function and that this function must be carried out by a conserved domain. We proceed to show that the Meinox domain, an N-terminal conserved domain shown to mediate Pbx binding, is sufficient to provide Meis activity to a Pbx/Hox complex. We find that this activity is separable from Pbx binding and resides within the M1 subdomain. This finding also presents a rational strategy for interfering with Meis activity in vivo. We accomplish this by expressing the Pbx4/Lzr N-terminus, which sequesters Meis proteins in the cytoplasm away from the nuclear transcription complexes. Sequestering Meis proteins in the cytoplasm leads to extensive loss of rhombomere (r) 3- and r4-specific gene expression, as well as defective rhombomere boundary formation in this region. These changes in gene expression correlate with impaired neuronal differentiation in r3 and r4, e.g. the loss of r3-specific nV branchiomotor neurons and r4-specific Mauthner neurons. We conclude that Meis family proteins are essential for the specification of r3 and r4 of the hindbrain.

scholarly journals Mitotic Spindle Integrity and Kinetochore Function Linked by the Duo1p/Dam1p Complex

2001 ◽  
Vol 152 (1) ◽  
pp. 197-212 ◽  
Author(s):  
Iain M. Cheeseman ◽  
Maria Enquist-Newman ◽  
Thomas Müller-Reichert ◽  
David G. Drubin ◽  
Georjana Barnes
Keyword(s):  
Mitotic Spindle ◽  
Genetic Interactions ◽  
Yeast Protein ◽  
Yeast Saccharomyces Cerevisiae ◽  
Chromosome Missegregation ◽  
Shared Function ◽  
Mutant Phenotypes ◽  
Bipolar Spindles ◽  
Kinetochore Function

Duo1p and Dam1p were previously identified as spindle proteins in the budding yeast, Saccharomyces cerevisiae. Here, analyses of a diverse collection of duo1 and dam1 alleles were used to develop a deeper understanding of the functions and interactions of Duo1p and Dam1p. Based on the similarity of mutant phenotypes, genetic interactions between duo1 and dam1 alleles, interdependent localization to the mitotic spindle, and Duo1p/Dam1p coimmunoprecipitation from yeast protein extracts, these analyses indicated that Duo1p and Dam1p perform a shared function in vivo as components of a protein complex. Duo1p and Dam1p are not required to assemble bipolar spindles, but they are required to maintain metaphase and anaphase spindle integrity. Immunofluorescence and electron microscopy of duo1 and dam1 mutant spindles revealed a diverse variety of spindle defects. Our results also indicate a second, previously unidentified, role for the Duo1p/Dam1p complex. duo1 and dam1 mutants show high rates of chromosome missegregation, premature anaphase events while arrested in metaphase, and genetic interactions with a subset of kinetochore components consistent with a role in kinetochore function. In addition, Duo1p and Dam1p localize to kinetochores in chromosome spreads, suggesting that this complex may serve as a link between the kinetochore and the mitotic spindle.

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