Evolution of Sequence, Structural and Functional Diversity of the Ubiquitous DNA/RNA-binding Alba Domain

Overview

Journal Sci Rep

Specialty Science

Date 2024 Dec 5

PMID 39638848

Authors

Jaiganesh Jagadeesh

Shruthi Sridhar Vembar

Affiliations

Soon will be listed here.

Abstract

The DNA/RNA-binding Alba domain is prevalent across all kingdoms of life. First discovered in archaea, this protein domain has evolved from RNA- to DNA-binding, with a concomitant expansion in the range of cellular processes that it regulates. Despite its widespread presence, the full extent of its sequence, structural, and functional diversity remains unexplored. In this study, we employed iterative searches in PSI-BLAST to identify 15,161 unique Alba domain-containing proteins from the NCBI non-redundant protein database. Sequence similarity network (SSN) analysis clustered them into 13 distinct subgroups, including the archaeal Alba and eukaryotic Rpp20/Pop7 and Rpp25/Pop6 groups, as well as novel fungal and Plasmodium-specific Albas. Sequence and structural conservation analysis of the subgroups indicated high preservation of the dimer interface, with Alba domains from unicellular eukaryotes notably exhibiting structural deviations towards their C-terminal end. Finally, phylogenetic analysis, while supporting SSN clustering, revealed the evolutionary branchpoint at which the eukaryotic Rpp20- and Rpp25-like clades emerged from archaeal Albas, and the subsequent taxonomic lineage-based divergence within each clade. Taken together, this comprehensive analysis enhances our understanding of the evolutionary history of Alba domain-containing proteins across diverse organisms.

Citing Articles

Ectopic overexpression of DNA-/RNA-binding Alba proteins misregulates virulence gene homeostasis during asexual blood development.

Acharya D, Bavikatte A, Ashok V, Hegde S, Macpherson C, Scherf A Microbiol Spectr. 2025; 13(3):e0088524.

PMID: 39868986 PMC: 11878077. DOI: 10.1128/spectrum.00885-24.

References

Orell A, Peeters E, Vassen V, Jachlewski S, Schalles S, Siebers B . Lrs14 transcriptional regulators influence biofilm formation and cell motility of Crenarchaea. ISME J. 2013; 7(10):1886-98. PMC: 3965304. DOI: 10.1038/ismej.2013.68. View

Bhatta A, Hillen H . Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes. Trends Biochem Sci. 2022; 47(11):965-977. DOI: 10.1016/j.tibs.2022.05.006. View

Tamura K, Battistuzzi F, Billing-Ross P, Murillo O, Filipski A, Kumar S . Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A. 2012; 109(47):19333-8. PMC: 3511068. DOI: 10.1073/pnas.1213199109. View

Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar G, Sonnhammer E . Pfam: The protein families database in 2021. Nucleic Acids Res. 2020; 49(D1):D412-D419. PMC: 7779014. DOI: 10.1093/nar/gkaa913. View

Zhang C, Shine M, Pyle A, Zhang Y . US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nat Methods. 2022; 19(9):1109-1115. DOI: 10.1038/s41592-022-01585-1. View

Lurz R, Grote M, Dijk J, Reinhardt R, Dobrinski B . Electron microscopic study of DNA complexes with proteins from the Archaebacterium Sulfolobus acidocaldarius. EMBO J. 1986; 5(13):3715-21. PMC: 1167416. DOI: 10.1002/j.1460-2075.1986.tb04705.x. View

Jarrous N . Roles of RNase P and Its Subunits. Trends Genet. 2017; 33(9):594-603. DOI: 10.1016/j.tig.2017.06.006. View

Zhang N, Guo L, Huang L . The Sac10b homolog from Sulfolobus islandicus is an RNA chaperone. Nucleic Acids Res. 2020; 48(16):9273-9284. PMC: 7498313. DOI: 10.1093/nar/gkaa656. View

Napoli A, Kvaratskelia M, White M, Rossi M, Ciaramella M . A novel member of the bacterial-archaeal regulator family is a nonspecific dna-binding protein and induces positive supercoiling. J Biol Chem. 2001; 276(14):10745-52. DOI: 10.1074/jbc.M010611200. View

10.

Frank D, Pace N . Ribonuclease P: unity and diversity in a tRNA processing ribozyme. Annu Rev Biochem. 1998; 67:153-80. DOI: 10.1146/annurev.biochem.67.1.153. View

11.

Steinegger M, Meier M, Mirdita M, Vohringer H, Haunsberger S, Soding J . HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics. 2019; 20(1):473. PMC: 6744700. DOI: 10.1186/s12859-019-3019-7. View

12.

Gissot M, Walker R, Delhaye S, Alayi T, Huot L, Hot D . Toxoplasma gondii Alba proteins are involved in translational control of gene expression. J Mol Biol. 2013; 425(8):1287-301. DOI: 10.1016/j.jmb.2013.01.039. View

13.

Naprstkova A, Malinska K, Drabkova L, Billey E, Naprstkova D, Sykorova E . Characterization of ALBA Family Expression and Localization in Generative Organs. Int J Mol Sci. 2021; 22(4). PMC: 7914821. DOI: 10.3390/ijms22041652. View

14.

Verma J, Gayali S, Dass S, Kumar A, Parveen S, Chakraborty S . OsAlba1, a dehydration-responsive nuclear protein of rice (Oryza sativa L. ssp. indica), participates in stress adaptation. Phytochemistry. 2014; 100:16-25. DOI: 10.1016/j.phytochem.2014.01.015. View

15.

Goyal M, Alam A, Iqbal M, Dey S, Bindu S, Pal C . Identification and molecular characterization of an Alba-family protein from human malaria parasite Plasmodium falciparum. Nucleic Acids Res. 2011; 40(3):1174-90. PMC: 3273813. DOI: 10.1093/nar/gkr821. View

16.

Chene A, Vembar S, Riviere L, Lopez-Rubio J, Claes A, Siegel T . PfAlbas constitute a new eukaryotic DNA/RNA-binding protein family in malaria parasites. Nucleic Acids Res. 2011; 40(7):3066-77. PMC: 3326326. DOI: 10.1093/nar/gkr1215. View

17.

Liu Y, Guo L, Guo R, Wong R, Hernandez H, Hu J . The Sac10b homolog in Methanococcus maripaludis binds DNA at specific sites. J Bacteriol. 2009; 191(7):2315-29. PMC: 2655493. DOI: 10.1128/JB.01534-08. View

18.

Li L, Banerjee A, Bischof L, Ramadan Maklad H, Hoffmann L, Henche A . Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius. Mol Microbiol. 2017; 105(5):777-793. DOI: 10.1111/mmi.13735. View

19.

Perederina A, Esakova O, Koc H, Schmitt M, Krasilnikov A . Specific binding of a Pop6/Pop7 heterodimer to the P3 stem of the yeast RNase MRP and RNase P RNAs. RNA. 2007; 13(10):1648-55. PMC: 1986809. DOI: 10.1261/rna.654407. View

20.

Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee G . Accurate prediction of protein structures and interactions using a three-track neural network. Science. 2021; 373(6557):871-876. PMC: 7612213. DOI: 10.1126/science.abj8754. View