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Biochemistry (Moscow)

, Volume 76, Issue 1, pp 131–146 | Cite as

Mutator effects and mutation signatures of editing deaminases produced in bacteria and yeast

  • A. G. Lada
  • C. Frahm Krick
  • S. G. Kozmin
  • V. I. Mayorov
  • T. S. Karpova
  • I. B. Rogozin
  • Y. I. PavlovEmail author
Article

Abstract

Enzymatic deamination of bases in DNA or RNA leads to an alteration of flow of genetic information. Adenosine deaminases edit RNA (ADARs, TADs). Specialized cytidine deaminases are involved in RNA/DNA editing in lipid metabolism (APOBEC1) and in innate (APOBEC3 family) and humoral (AID) immunity. APOBEC2 is required for proper muscle development and, along with AID, was implicated in demethylation of DNA. The functions of APOBEC4, APOBEC5, and other deaminases recently discovered by bioinformatics approaches are unknown. What is the basis for the diverse biological functions of enzymes with similar enzyme structure and the same principal enzymatic reaction? AID, APOBEC1, lamprey CDA1, and APOBEC3G enzymes cause uracil DNA glycosylase-dependent induction of mutations when overproduced ectopically in bacteria or yeast. APOBEC2, on the contrary, is nonmutagenic. We studied the effects of the expression of various deaminases in yeast and bacteria. The mutagenic specificities of four deaminases, hAID, rAPOBEC1, hAPOBEC3G, and lamprey CDA1, are strikingly different. This suggests the existence of an intrinsic component of deaminase targeting. The expression of yeast CDD1 and TAD2/TAD3, human APOBEC4, Xanthomonas oryzae APOBEC5, and deaminase encoded by Micromonas sp. gene MICPUN_56782 was nonmutagenic. A lack of a mutagenic effect for Cdd1 is expected because the enzyme functions in the salvage of pyrimidine nucleotides, and it is evolutionarily distant from RNA/DNA editing enzymes. The reason for inactivity of deaminases grouped with APOBEC2 is not obvious from their structures. This cannot be explained by protein insolubility and peculiarities of cellular distribution and requires further investigation.

Key words

editing deaminases mutagenesis immunity DNA repair 

Abbreviations

ADA

adenosine deaminase

AID

activation induced deaminase

Apn

apurinic/apyrimidinic nuclease

APOBEC

apolipoprotein B editase complex related enzyme

AP

site, apurinic/apyrimidinic site

CDA or CDD

cytidine deaminase or various organisms

CSR

class switch recombination

GC

gene conversion

GFP

green fluorescent protein

HIV

human immunodeficiency virus

IPTG

isopropyl-β-D-1-thiogalactopyranoside

LB

Luria-Bertani medium

LDS

lithium dodecyl sulfate

LRR

leucine-rich repeats

Nfi

endonuclease five

NLS

nuclear localization signal

ORF

open reading frame

PmCDA

Pteromyzon marinus cytidine deaminase

SC

synthetic medium for yeast cultivation

SDS

sodium dodecyl sulfate

SHM

somatic hypermutation

Tad

tRNA adenosine deaminase

UNG or UDG

uracil-N-glycosylase or uracil-DNA-glycosylase

Vif

virus infectivity factor

VLR

variable lymphocyte receptors

YEPD

complete medium for yeast cultivation

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Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  • A. G. Lada
    • 1
  • C. Frahm Krick
    • 1
  • S. G. Kozmin
    • 2
  • V. I. Mayorov
    • 3
  • T. S. Karpova
    • 4
  • I. B. Rogozin
    • 5
    • 6
  • Y. I. Pavlov
    • 1
    Email author
  1. 1.Eppley Institute for Research in Cancer and Allied DiseasesUniversity of Nebraska Medical CenterOmahaUSA
  2. 2.Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamUSA
  3. 3.Mercer University School of MedicineMaconUSA
  4. 4.Laboratory of Receptor Biology and Gene ExpressionNational Cancer Institute, Center for Cancer Research Core Imaging FacilityBethesdaUSA
  5. 5.National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaUSA
  6. 6.Institute of Cytology and GeneticsNovosibirskRussia

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