Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences DOI Creative Commons
Sushmita Basu, Jing Yu, Daisuke Kihara

и другие.

Briefings in Bioinformatics, Год журнала: 2024, Номер 26(1)

Опубликована: Ноя. 22, 2024

Abstract Computational prediction of nucleic acid-binding residues in protein sequences is an active field research, with over 80 methods that were released the past 2 decades. We identify and discuss 87 sequence-based predictors include dozens recently published are surveyed for first time. overview historical progress examine multiple practical issues availability impact predictors, key features their predictive models, important aspects related to training assessment. observe decade has brought increased use deep neural networks language which contributed substantial gains performance. also highlight advancements vital challenging cross-predictions between deoxyribonucleic acid (DNA)-binding ribonucleic (RNA)-binding targeting two distinct sources binding annotations, structure-based versus intrinsic disorder-based. The trained on structure-annotated interactions tend perform poorly disorder-annotated vice versa, only a few target well across both annotation types. significant problem, some DNA-binding or RNA-binding indiscriminately predicting Moreover, we show web servers cited substantially more than tools without implementation no longer working implementations, motivating development long-term maintenance servers. close by discussing future research directions aim drive further this area.

Язык: Английский

Protein Disorder in Plant Stress Adaptation: From Late Embryogenesis Abundant to Other Intrinsically Disordered Proteins DOI Open Access
An‐Shan Hsiao

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(2), С. 1178 - 1178

Опубликована: Янв. 18, 2024

Global climate change has caused severe abiotic and biotic stresses, affecting plant growth food security. The mechanical understanding of stress responses is critical for achieving sustainable agriculture. Intrinsically disordered proteins (IDPs) are a group without unique three-dimensional structures. environmental sensitivity structural flexibility IDPs contribute to the developmental plasticity sessile plants deal with challenges. This article discusses roles various in tolerance resistance, describes current mechanistic insights into unstructured such as disorder-to-order transition adopting secondary structures interact specific partners (i.e., cellular membranes, membrane proteins, metal ions, DNA), elucidates liquid–liquid phase separation driven by protein disorder responses. By comparing IDP studies animal systems, this provides conceptual principles adaptation, reveals research gaps, advises on future direction. highlighting relevant unanswered questions aims encourage more these emerging topics understand mechanisms action behind their resistance phenotypes.

Язык: Английский

Процитировано

11
Teleost genomic repeat landscapes in light of diversification rates and ecology DOI Creative Commons
William B. Reinar, Ole K. Tørresen, Alexander J. Nederbragt

и другие.

Mobile DNA, Год журнала: 2023, Номер 14(1)

Опубликована: Окт. 3, 2023

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering major branches diverse lineage teleost fish. We investigated if TE correlates family level net diversification rates and found support for weak negative correlation. Further, demonstrated that proportion size, but not to short tandem repeats (STRs), which implies independent evolutionary paths. Marine freshwater fish had large differences STR content, extreme propagation detected genomes codfish Atlantic herring. Such high density STRs is likely increase mutational load, propose could be counterbalanced by fecundity as seen codfishes

Язык: Английский

Процитировано

15
Molecular characterization of genes involved in tolerance of cadmium in Triticum aestivum (L.) under Cd stress DOI

Asima Rasheed,

Arwa Abdulkreem AL‐Huqail, Baber Ali

и другие.

Journal of Hazardous Materials, Год журнала: 2023, Номер 464, С. 132955 - 132955

Опубликована: Ноя. 10, 2023

Язык: Английский

Процитировано

14
Cell wall‐resident proteins with internal repeats (PIRs) show an inverted architecture in Neurospora crassa, but maintain their role as wall stabilizers DOI Open Access
Paul Montaño‐Silva, Olga A. Callejas‐Negrete, Alejandro Pereira‐Santana

и другие.

FEBS Journal, Год журнала: 2025, Номер unknown

Опубликована: Фев. 13, 2025

Proteins with internal repeats (PIRs) are the second most abundant class of fungal cell wall resident proteins. In yeasts, PIRs preserve stability under stressful conditions. They characterized by conserved N‐terminal amino acid sequences repeated in tandem (PIR motifs), and a cysteine (Cys)‐rich C‐terminal domain. have been identified several filamentous fungi genomes; however, they not studied beyond yeasts. this work, diversity, evolution, biological role PIRs, particular focus on new class, was addressed. Bioinformatic inference indicated were an innovation Ascomycota. Predicted clustered two main groups: classical yeasts (N‐terminal PIR motifs; Cys‐rich domain), from inverted architecture domain; which could harbor additional glycosylphosphatidylinositol (GPI) addition‐signals. As representatives group, Neurospora crassa (Nc) PIR‐1 (NCU04033) PIR‐2 (NCU07569) studied. Confocal microscopy eGFP‐labeled Nc revealed accumulate apical plugs; additionally, requires Kex2 processing site for correct maturation harbors predicted GPI modification signal. Moreover, Δpir‐1 Δpir‐2 single mutants showed growth rate similar to that wild‐type (WT), but double mutant / grew significantly slower. Similarly, mildly sensitive calcofluor white, although Δ pir‐1 /Δ pir‐2 severely impaired. Despite PIR‐2, maintain as stabilizers like yeast PIRs.

Язык: Английский

Процитировано

0
Tandem repeat polymorphisms shape local adaptation DOI
David G. King

Trends in Ecology & Evolution, Год журнала: 2025, Номер 40(4), С. 331 - 334

Опубликована: Март 5, 2025

Язык: Английский

Процитировано

0
Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations DOI

Xiyu Tan,

Wanyong Zeng,

Yujian Yang

и другие.

Journal of genetics and genomics/Journal of Genetics and Genomics, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

Процитировано

0
Simple sequence repeats and their expansions: role in plant development, environmental response and adaptation DOI Creative Commons
Sridevi Sureshkumar, Aaryan Chhabra, Ya‐Long Guo

и другие.

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Май 5, 2025

Summary Repetitive DNA is a feature of all organisms, ranging from archaea and plants to humans. repeats can be seen both in coding noncoding regions the genome. Due recurring nature sequences, simple tend more prone errors during replication repair, resulting variability their unit length. This sequence led use as molecular markers for mapping traits diverse organisms. Advances genomics, ever‐reducing costs genome sequencing have empowered us assess functional impacts repeats. The repeat lengths cause phenotypic differences depending on where they are present Variability length genes results poly amino acid stretches that appear interfere with protein function, including perturbation protein–protein interactions impacts. These often common allelic variations significantly impact evolutionary dynamics. In extreme situations, undergo massive expansions outliers. Repeat underlie several genetic defects diseases review systematically analyses tandem plants, role development environmental response adaptation plants. We identify synthesise emerging themes, differentiate expansions, argue many repeat‐associated phenotypes yet discovered. emphasise underexplored immense potential this area research, particularly suggest ways which achieved how it might contribute evolution agricultural productivity.

Язык: Английский

Процитировано

0
The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758) DOI Creative Commons
Sissel Jentoft, Ole K. Tørresen,

Ave Tooming‐Klunderud

и другие.

Wellcome Open Research, Год журнала: 2024, Номер 9, С. 189 - 189

Опубликована: Апрель 12, 2024

We present a genome assembly from an individual male

Язык: Английский

Процитировано

3
Clinal Variation in Short Tandem Repeats Linked to Gene Expression in Sunflower (Helianthus annuus L.) DOI Creative Commons
Chathurani Ranathunge, Mark E. Welch

Biomolecules, Год журнала: 2024, Номер 14(8), С. 944 - 944

Опубликована: Авг. 3, 2024

Short tandem repeat (STR) variation is rarely explored as a contributor to adaptive evolution. An intriguing mechanism involving STRs suggests that function “tuning knobs” of adaptation whereby stepwise changes in STR allele length have effects on phenotypes. Previously, we tested the predictions knob” model at gene expression level by conducting an RNA-Seq experiment natural populations common sunflower (Helianthus annuus L.) transecting well-defined cline from Kansas Oklahoma. We identified 479 with significant (eSTRs). In this study, expanded range further north and south focal used targeted approach study relationship between five selected eSTRs. Seeds 96 individuals six Nebraska Texas were grown garden. The genotyped eSTRs, was quantified qRT-PCR. Linear regression models eSTR comp26672 significantly correlated expression. Further, latitude across Texas. locus located CHUP1 gene, associated chloroplast movement response light intensity, which potential role for locus. Collectively, our results show consistent some eSTRs broad geographical suggest may contribute traits sunflower.

Язык: Английский

Процитировано

2
Structured Tandem Repeats in Protein Interactions DOI Open Access
Juan Mac Donagh, Abril Marchesini,

Agostina Spiga

и другие.

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(5), С. 2994 - 2994

Опубликована: Март 5, 2024

Tandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit ensemble packs against first one. Here, we examine TR proteins (TRPs) to see how their sequence, structure, and evolutionary properties favor them for function as mediators interactions. Our observations suggest TRPs bind other using large, structured surfaces like globular domains; particular, open-structured ensembles favored by flexible termini possibility tightly coil targets. While, intuitively, open seem prone evolve due potential accommodate insertions deletions units, these events unexpectedly rare, suggesting they advantageous emergence ancestral but early fixed. We hypothesize flexibility makes it easier further adapt interact with them, which would explain large number provide insight make scaffolds alternative complexes organize genes, RNA proteins.

Язык: Английский

Процитировано

2