The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

Xuan, Jinsong; Feng, Yingang

doi:10.2174/138920312800785067

Cited by 10 publications

(8 citation statements)

References 55 publications

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“…The DNA-binding Alba (acetylation lowers binding affinity) superfamily of proteins has received global attention immediately after the Alba proteins were identified from archaea as sequence-independent DNA-binding proteins [ 4 , 5 , 6 ]. The members of this superfamily are diversely found in archaea and eukaryotes as small, basic, dimeric nucleic acid-binding proteins [ 7 , 8 , 9 , 10 , 11 ]. Although Alba proteins behave as histone-like DNA-binding components, RNA-binding properties of Alba have also been reported [ 4 , 6 , 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes

Verma

Wardhan

Singh

et al. 2018

Genes

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Architectural proteins play key roles in genome construction and regulate the expression of many genes, albeit the modulation of genome plasticity by these proteins is largely unknown. A critical screening of the architectural proteins in five crop species, viz., Oryza sativa, Zea mays, Sorghum bicolor, Cicer arietinum, and Vitis vinifera, and in the model plant Arabidopsis thaliana along with evolutionary relevant species such as Chlamydomonas reinhardtii, Physcomitrella patens, and Amborella trichopoda, revealed 9, 20, 10, 7, 7, 6, 1, 4, and 4 Alba (acetylation lowers binding affinity) genes, respectively. A phylogenetic analysis of the genes and of their counterparts in other plant species indicated evolutionary conservation and diversification. In each group, the structural components of the genes and motifs showed significant conservation. The chromosomal location of the Alba genes of rice (OsAlba), showed an unequal distribution on 8 of its 12 chromosomes. The expression profiles of the OsAlba genes indicated a distinct tissue-specific expression in the seedling, vegetative, and reproductive stages. The quantitative real-time PCR (qRT-PCR) analysis of the OsAlba genes confirmed their stress-inducible expression under multivariate environmental conditions and phytohormone treatments. The evaluation of the regulatory elements in 68 Alba genes from the 9 species studied led to the identification of conserved motifs and overlapping microRNA (miRNA) target sites, suggesting the conservation of their function in related proteins and a divergence in their biological roles across species. The 3D structure and the prediction of putative ligands and their binding sites for OsAlba proteins offered a key insight into the structure–function relationship. These results provide a comprehensive overview of the subtle genetic diversification of the OsAlba genes, which will help in elucidating their functional role in plants.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes

Verma

Wardhan

Singh

et al. 2018

Genes

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“…Alba (Acetylation lowers binding affinity, reviewed in [ 30 ]) is a family of small, abundant DNA binding proteins (whose members are also known as Sac10 or Sso10, Ape10 etc. ).…”

Section: Architectual Proteins Of Hyperthermophilic Archaeamentioning

confidence: 99%

Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

Visone

Vettone

Serpe

et al. 2014

IJMS

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In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

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“…S. solfataricus is the most widely investigated of the organisms in the crenarchaeal branch of the archaea and has been used as a model for studies of the mechanisms of DNA replication, the cell cycle, chromosomal integration, transcription, RNA processing and translation. A number of small-molecule DNA-binding proteins have been studied in S. solfataricus, including the 7, 8 and 10 kDa class protein families (White & Bell, 2002;Sandman & Reeve, 2005;Xuan & Feng, 2012). However, there are still genes with unknown function in the S. solfataricus genome.…”

Section: Introductionmentioning

confidence: 99%

Crystal structure of the programmed cell death 5 protein from Sulfolobus solfataricus

et al. 2019

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Programmed cell death 5 (PDCD5) is a vital signaling protein in the apoptosis pathway in eukaryotes. It is known that there are two dissociated N‐terminal regions and a triple‐helix core in eukaryotic PDCD5. Structural and functional studies of PDCD5 from hyperthermophilic archaea have been limited to date. Here, the PDCD5 homolog Sso0352 (SsoPDCD5) was identified in Sulfolobus solfataricus, the SsoPDCD5 protein was expressed and crystallized, and the phase was identified by single‐wavelength anomalous diffraction. The native SsoPDCD5 crystal belonged to space group C2 and diffracted to 1.49 Å resolution. This is the first crystal structure of a PDCD5 homolog to be solved. SsoPDCD5 shares a similar triple‐helix bundle with eukaryotic PDCD5 but has a long α‐helix in the N‐terminus. A structural search and biochemical data suggest that SsoPDCD5 may function as a DNA‐binding protein.

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The Archaeal Sac10b Protein Family: Conserved Proteins with Divergent Functions

Cited by 10 publications

References 55 publications

Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes

Genome-Wide Identification of the Alba Gene Family in Plants and Stress-Responsive Expression of the Rice Alba Genes

Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

Crystal structure of the programmed cell death 5 protein from Sulfolobus solfataricus

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