Correction: The microprotein Nrs1 rewires the G1/S transcriptional machinery during nitrogen limitation in budding yeast DOI Creative Commons

PLoS Biology, Год журнала: 2022, Номер 20(3), С. e3001595 - e3001595

Опубликована: Март 8, 2022

[This corrects the article DOI: 10.1371/journal.pbio.3001548.].

Язык: Английский

BBX30/miP1b and BBX31/miP1a form a positive feedback loop with ABI5 to regulate ABA‐mediated postgermination seedling growth arrest DOI
Deeksha Singh, Sourav Datta

New Phytologist, Год журнала: 2023, Номер 238(5), С. 1908 - 1923

Опубликована: Март 8, 2023

Summary In plants, the switch to autotrophic growth involves germination followed by postgermination seedling establishment. When environmental conditions are not favorable, stress hormone abscisic acid (ABA) signals plants postpone establishment inducing expression of transcription factor ABI5. The levels ABI5 determine efficiency ABA‐mediated developmental arrest. molecular mechanisms regulating stability and activity during transition light less known. Using genetic, molecular, biochemical approach, we found that two B‐box domain containing proteins BBX31 BBX30 alongwith inhibit in a partially interdependent manner. also characterized as microProteins miP1a miP1b, respectively, based on their small size, single domain, ability interact with multidomain proteins. miP1a/BBX31 miP1b/BBX30 physically stabilize it promote its binding promoters downstream genes. reciprocally induces directly promoter. thereby form positive feedback loop arrest seedlings.

Язык: Английский

Процитировано

15

Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast DOI Creative Commons
Niklas F. C. Hummel, Kasey Markel, Jordan Stefani

и другие.

Cell Systems, Год журнала: 2024, Номер 15(7), С. 662 - 672.e4

Опубликована: Июнь 13, 2024

Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped domains in transcription but not non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the domain predictor PADDLE to analyze proteomes of Arabidopsis thaliana Saccharomyces cerevisiae. We screened 18,000 predicted from >800 genes both species, confirming that 89% candidate contain active fragments. Our work enables annotation hundreds nuclear as putative coactivators, many which never been ascribed any function plants. Analysis peptide sequence compositions reveals how distribution key amino acids dictates activity. Finally, validated short, "universal" with comparable performance state-of-the-art used for genome engineering. approach genome-wide discovery across diverse eukaryotes.

Язык: Английский

Процитировано

6

What programs the size of animal cells? DOI Creative Commons
Shixuan Liu, Ceryl Tan, Mike Tyers

и другие.

Frontiers in Cell and Developmental Biology, Год журнала: 2022, Номер 10

Опубликована: Ноя. 1, 2022

The human body is programmed with definite quantities, magnitudes, and proportions. At the microscopic level, such sizes manifest in individual cells - different cell types are characterized by distinct whereas of same type highly uniform size. How do a population maintain uniformity size, how changes target size programmed? A convergence recent historical studies suggest just as thermostat maintains room temperature proliferating animal similarly maintained homeostatic mechanisms. In this review, we first summarize old new literature on existence checkpoints, then discuss additional advances study homeostasis that involve feedback regulation cellular growth rate. We further progress molecules underlie checkpoints mechanisms specify setpoints. Lastly, less-well explored teleological question: why does matter what functional importance control?

Язык: Английский

Процитировано

17

Swi4-dependent SWI4 transcription couples cell size to cell cycle commitment DOI Creative Commons
Pooja Goswami, Abhishek Ghimire,

Carleton H. Coffin

и другие.

iScience, Год журнала: 2025, Номер 28(3), С. 112027 - 112027

Опубликована: Фев. 13, 2025

Язык: Английский

Процитировано

0

Discovering the hidden function in fungal genomes DOI Creative Commons
Nicholas C. Gervais, Rebecca S. Shapiro

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Сен. 19, 2024

Язык: Английский

Процитировано

2

Casting CRISPR-Cas13d to fish for microprotein functions in animal development DOI Creative Commons
Anthony J. Treichel, Ariel Bazzini

iScience, Год журнала: 2022, Номер 25(12), С. 105547 - 105547

Опубликована: Ноя. 10, 2022

Protein coding genes were originally identified with sequence-based definitions that included a 100-codon cutoff to avoid annotating irrelevant open reading frames. However, many active proteins contain less than 100 amino acids. Indeed, functional genetics, ribosome profiling, and proteomic profiling have short, translated frames, including those biologically peptide products (microproteins). Yet, functions for most of these remain unknown. Because microproteins often act as key signals or fine-tune processes, animal development has already revealed handful provides an ideal context uncover additional microprotein functions. mRNAs during early are maternally provided hinder targeted mutagenesis approaches characterize developmental The recently established, RNA-targeting CRISPR-Cas13d system in zebrafish overcomes this barrier produces potent knockdown mRNA, enables flexible, efficient interrogation development.

Язык: Английский

Процитировано

7

Absolute quantification of protein number and dynamics in single cells DOI Creative Commons
Catherine A. Royer, Mike Tyers, Sylvain Tollis

и другие.

Current Opinion in Structural Biology, Год журнала: 2023, Номер 82, С. 102673 - 102673

Опубликована: Авг. 16, 2023

Язык: Английский

Процитировано

1

Methods for Analysis of Interactome of Microproteins Encoded by Short Open Reading Frames DOI
Ilya A. Sedlov, Igor Fesenko

Russian Journal of Bioorganic Chemistry, Год журнала: 2023, Номер 49(4), С. 717 - 730

Опубликована: Авг. 1, 2023

Язык: Английский

Процитировано

1

Systematic identification of transcriptional activator domains from non-transcription factor proteins in plants and yeast DOI Open Access
Niklas F. C. Hummel, Kasey Markel, Jordan Stefani

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Сен. 12, 2023

Abstract Transcription factors promote gene expression via trans-regulatory activation domains. Although whole genome scale screens in model organisms (e.g. human, yeast, fly) have helped identify domains from transcription factors, such been less extensively used to explore the occurrence of non-transcription factor proteins, as transcriptional coactivators, chromatin regulators and some cytosolic leaving a blind spot on what role these proteins could play regulating transcription. We utilized domain predictor PADDLE mine entire proteomes two eukaryotes, Arabidopsis thaliana Saccharomyces cerevisiae ( 1 ). characterized 18,000 fragments covering predicted >800 genes both species, experimentally validated that 89% contained capable activating yeast. Peptides with similar sequence composition show broad range activities, which is explained by arrangement key amino acids. also annotated hundreds nuclear putative coactivators; many never ascribed any function plants. Furthermore, our library contains >250 non-nuclear containing peptides across eukaryotic lineages, suggesting there are unknown biological roles beyond Finally, we validate short, ‘universal’ activate yeast plants comparable or stronger performance state-of-the-art Overall, dual host screen provides blueprint how systematically discover novel genetic parts for synthetic biology wide diversity eukaryotes. Significance Statement Activation critical expression. mapping has carried out previous genome-wide screens, their explored. utilize an new proteins. derived >750 transcription, discovering potentially coactivators Importantly, can representing unique tools.

Язык: Английский

Процитировано

1

Biochemistry and Protein Interactions of the CYREN Microprotein DOI

Lina Xie,

M.E. Bowman,

Gordon V. Louie

и другие.

Biochemistry, Год журнала: 2023, Номер 62(21), С. 3050 - 3060

Опубликована: Окт. 9, 2023

Over the past decade, advances in genomics have identified thousands of additional protein-coding small open reading frames (smORFs) missed by traditional gene finding approaches. These smORFs encode peptides and proteins, commonly termed micropeptides or microproteins. Several these newly discovered microproteins biological functions operate through interactions with proteins protein complexes within cell. CYREN1 is a characterized microprotein that regulates double-strand break repair mammalian cells interaction Ku70/80 heterodimer. binds to stabilizes breaks recruits machinery needed for nonhomologous end join repair. In this study, we examined biochemical properties better understand explain its cellular interactions. Our findings support an intrinsically disordered structure allows it enriches several including SF3B1 via distinct short linear motif (SLiMs) on CYREN1. Since many are predicted be disordered, exemplar how interact other reveals unknown scaffolding function may link NHEJ splicing.

Язык: Английский

Процитировано

1