Evolutionary history of Ku proteins: evidence of horizontal gene transfer from archaea to eukarya

Abstract Background The DNA end joining protein, Ku, is essential in Non-Homologous End Joining in prokaryotes and eukaryotes. It was first discovered in eukaryotes and later by PSI blast, was discovered in prokaryotes. While Ku in eukaryotes is often a multi domain protein functioning in DNA repair of physiological and pathological DNA double stranded breaks, Ku in prokaryotes is a single domain protein functioning in pathological DNA repair in spores or late stationary phase. In this paper we have attempted to systematically search for Ku protein in different phyla of bacteria and archaea as well as in different kingdoms of eukarya. Result From our search of 116 sequenced bacterial genomes, only 25 genomes yielded at least one Ku sequence. From a comprehensive search of all NCBI archaeal genomes, we received a positive hit in 7 specific archaea that possessed Ku. In eukarya, we found Ku protein in 27 out of 59 species. Since the entire genome of all eukaryotic species is not fully sequenced this number could go up. We then drew a phylogenetic maximum likelihood tree to determine the ancestral relationship between Ku70 and Ku80 in eukaryotes and Ku in prokaryotes. Out tree revealed a common node for some archaeal Ku, Ku70 and Ku80. Conclusion This led us to hypothesize that Ku from archaea transferred through horizontal gene transfer onto neozoa and then duplicated to form Ku70 and Ku80. Additionally, we analyzed the domains of the different eukaryotic species to demonstrate that fusion, fission, terminal addition, terminal deletion, single domain loss, single domain emergence events during evolution.

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The Speed of Allosteric Signaling Within a Single-Domain Protein

The Journal of Physical Chemistry Letters ◽

10.1021/acs.jpclett.1c00915 ◽

2021 ◽

pp. 4262-4267

Author(s):

Olga Bozovic ◽

Jeannette Ruf ◽

Claudio Zanobini ◽

Brankica Jankovic ◽

David Buhrke ◽

...

Keyword(s):

Single Domain ◽

Single Domain Protein ◽

Domain Protein

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Low Force Unfolding of a Single-Domain Protein by Parallel Pathways

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.0c11308 ◽

2021 ◽

Vol 125 (7) ◽

pp. 1799-1805

Author(s):

Pavel I. Zhuravlev ◽

Michael Hinczewski ◽

D. Thirumalai

Keyword(s):

Single Domain ◽

Single Domain Protein ◽

Parallel Pathways ◽

Domain Protein

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Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms

PLoS ONE ◽

10.1371/journal.pone.0001055 ◽

2007 ◽

Vol 2 (10) ◽

pp. e1055 ◽

Cited By ~ 47

Author(s):

Saliou Fall ◽

Anne Mercier ◽

Franck Bertolla ◽

Alexandra Calteau ◽

Laurent Gueguen ◽

...

Keyword(s):

Dna Repair ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Dna Repair Mechanisms ◽

Repair Mechanisms

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The Protease ClpXP and the PAS Domain Protein DivL Regulate CtrA and Gene Transfer Agent Production inRhodobacter capsulatus

Applied and Environmental Microbiology ◽

10.1128/aem.00275-18 ◽

2018 ◽

Vol 84 (11) ◽

Cited By ~ 9

Author(s):

Alexander B. Westbye ◽

Lukas Kater ◽

Christina Wiesmann ◽

Hao Ding ◽

Calvin K. Yip ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Rhodobacter Capsulatus ◽

Caulobacter Crescentus ◽

Response Regulator ◽

Pas Domain ◽

Content Type ◽

Regulatory Systems ◽

Gene Transfer Agent ◽

Domain Protein

ABSTRACTSeveral members of theRhodobacterales(Alphaproteobacteria) produce a conserved horizontal gene transfer vector, called the gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system used to study GTA biology is theRhodobacter capsulatusGTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in theAlphaproteobacteriaand is an essential regulator of RcGTA production: it controls the production and maturation of the RcGTA particle and RcGTA release from cells. CtrA also controls the natural transformation-like system required for cells to receive RcGTA-donated DNA. Here, we report that dysregulation of the CckA-ChpT-CtrA phosphorelay either by the loss of the PAS domain protein DivL or by substitution of the autophosphorylation residue of the hybrid histidine kinase CckA decreased CtrA phosphorylation and greatly increased RcGTA protein production inR. capsulatus. We show that the loss of the ClpXP protease or the three C-terminal residues of CtrA results in increased CtrA levels inR. capsulatusand identify ClpX(P) to be essential for the maturation of RcGTA particles. Furthermore, we show that CtrA phosphorylation is important for head spike production. Our results provide novel insight into the regulation of CtrA and GTAs in theRhodobacterales.IMPORTANCEMembers of theRhodobacteralesare abundant in ocean and freshwater environments. The conserved GTA produced by manyRhodobacteralesmay have an important role in horizontal gene transfer (HGT) in aquatic environments and provide a significant contribution to their adaptation. GTA production is controlled by bacterial regulatory systems, including the conserved CckA-ChpT-CtrA phosphorelay; however, several questions about GTA regulation remain. Our identification that a short DivL homologue and ClpXP regulate CtrA inR. capsulatusextends the model of CtrA regulation fromCaulobacter crescentusto a member of theRhodobacterales. We found that the magnitude of RcGTA production greatly depends on DivL and CckA kinase activity, adding yet another layer of regulatory complexity to RcGTA. RcGTA is known to undergo CckA-dependent maturation, and we extend the understanding of this process by showing that the ClpX chaperone is required for formation of tailed, DNA-containing particles.

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