The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism

  title={The two faces of Alba: the evolutionary connection between proteins participating in chromatin structure and RNA metabolism},
  author={L. Aravind and Lakshminarayan M. Iyer and Vivek Anantharaman},
  journal={Genome Biology},
  pages={R64 - R64}
BackgroundThere is considerable heterogeneity in the phyletic patterns of major chromosomal DNA-binding proteins in archaea. Alba is a well-characterized chromosomal protein from the crenarchaeal genus Sulfolobus. While Alba has been detected in most archaea and some eukaryotic taxa, its exact functions in these taxa are not clear. Here we use comparative genomics and sequence profile analysis to predict potential alternative functions of the Alba proteins.ResultsUsing sequence-profile searches… 

Structural and evolutionary analysis of Leishmania Alba proteins.

The archaeal Sac10b protein family: conserved proteins with divergent functions.

The present state of structural and functional studies of the Sac10b protein family, a class of highly conserved 10 kDa nucleic acid-binding proteins in archaea, is reviewed and existing and new X-ray and NMR structures of individual hyperthermophilic Sac10B proteins may represent very good models for introducing thermostability especially in enzymes for industrial use.

The CRM domain: an RNA binding module derived from an ancient ribosome-associated protein.

It is suggested that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes.

PfAlbas constitute a new eukaryotic DNA/RNA-binding protein family in malaria parasites

It is demonstrated for the first time in eukaryotes that Alba-like proteins bind to both DNA and RNA and that their intracellular location is developmentally regulated.

The function of KptA/Tpt1 gene - a minor review.

The gene structure, the evolution history and the function of KptA/Tpt1 from prokaryote to eukaryote organisms is concluded, and some proposals to clarify unclear problems of it in the future are given.

CC1, a Novel Crenarchaeal DNA Binding Protein (cid:1)

CC1 is a 6-kDa, monomeric, basic protein that is expressed at a high level in T. tenax and is very closely related to one another, and homologs are restricted to the P. aerophilum and Aeropyrum pernix genomes.

Alba-Domain Proteins of Trypanosoma brucei Are Cytoplasmic RNA-Binding Proteins That Interact with the Translation Machinery

The identification of 3 Alba-domain proteins is consistent with stage-specific regulation of translation in trypanosomes, but most likely in the context of initiation.

Differential Subcellular Localization of Leishmania Alba-Domain Proteins throughout the Parasite Development

Shuttling of Alba-domain proteins between the cytoplasm and the nucleolus or the flagellum throughout the parasite life cycle suggests that these RNA-binding proteins participate in several distinct regulatory pathways controlling developmental gene expression in Leishmania.



The Interaction of Alba, a Conserved Archaeal Chromatin Protein, with Sir2 and Its Regulation by Acetylation

Sir2 can deacetylate Alba and mediate transcriptional repression in a reconstituted in vitro transcription system, providing a paradigm for how Sir2 family proteins influence transcription and suggesting that modulation of chromatin structure by acetylation arose before the divergence of the archaeal and eukaryotic lineages.

Structure of Alba: an archaeal chromatin protein modulated by acetylation

A model for the Alba–DNA interaction is presented consistent with the available structural, biophysical and electron microscopy data.

Comparative genomics and evolution of proteins involved in RNA metabolism.

A comprehensive, genome-wide census of all enzymatic and non-enzymatic protein domains involved in RNA metabolism was conducted by using sequence profile analysis and structural comparisons, which reconstructed the principal features of LUCA's RNA metabolism system by parsimony-based evolutionary analysis of all relevant groups of orthologous proteins.

A PIWI homolog is one of the proteins expressed exclusively during macronuclear development in the ciliate Stylonychia lemnae.

One gene, mdp1 [macronuclear development protein 1 (MDP1)], encodes a homolog of the PIWI protein family, which is involved in germline differentiation processes and RNA silencing in worms, flies, mice, humans and in plants.

Identification of the gene encoding archeal‐specific DNA‐binding proteins of the Sac10b family

Binding of proteins of this family leads to significant bending and unwinding of DNA and induces negative supercoils, suggesting a role in DNA compaction in Sulfolobus, and an homologue of ssh10b in all archaeal genomes is found.

Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach.

It is suggested that in archaea, a tight functional coupling exists between translation, RNA processing and degradation, (apparently mediated by the predicted exosome) and protein degradation (mediated by the proteasome), and may have implications for cross-talk between these processes in eukaryotes.

Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box.

The cloning and sequencing of a cDNA encoding the hnRNP U protein is described, the determination of its amino acid sequence and the delineation of a region in this protein that confers RNA binding are described, and an RNA binding activity is identified within the C‐terminal glycine‐rich 112 amino acids.

CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin.

The molecular cloning of the crs1 gene is reported and an initial biochemical characterization of its gene product is reported, supporting the notion that CRS1 is a bona fide group II intron splicing factor.

Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP.

The degree of structural similarity between nuclear RNase P and RNase MRP suggests that some aspects of their functions in pre-tRNA and pre-rRNA processing pathways might overlap or be coordinated.