C2H2 zinc finger proteins of the SP/KLF, Wilms tumor, EGR, Huckebein, and Klumpfuss families in metazoans and beyond

Jimin Pei, Nick V. Grishin

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Specificity proteins (SPs) and Krüppel-Like Factors (KLFs) are C2H2-type zinc finger transcription factors that play essential roles in differentiation, development, proliferation and cell death. SP/KLF proteins, similarly to Wilms tumor protein 1 (WT1), Early Growth Response (EGR), Huckebein, and Klumpfuss, prefer to bind GC-rich sequences such as GC-box and CACCC-box (GT-box). We searched various genomes and transcriptomes of metazoans and single-cell holozoans for members of these families. Seven groups of KLFs (KLFA-G) and three groups of SPs (SPA-C) were identified in the three lineages of Bilateria (Deuterostomia, Ecdysozoa, and Lophotrochozoa). The last ancestor of jawed vertebrates was inferred to have at least 18 KLFs (group A: KLF1/2/4/17, group B: KLF3/8/12; group C: KLF5/5l; group D: KLF6/7; group E: KLF9/13/16; group F: KLF10/KLF11; group G: KLF15/15l) and 10 SPs (group A: SP1/2/3/4; group B: SP5/5l; group C: SP6/7/8/9), since they were found in both cartilaginous and boned fishes. Placental mammals have added KLF14 (group E) and KLF18 (group A), and lost KLF5l (KLF5-like) and KLF15l (KLF15-like). Multiple KLF members were found in basal metazoans (Ctenophora, Porifera, Placozoa, and Cnidaria). Ctenophora has the least number of KLFs and no SPs, which could be attributed to its proposed sister group relationship to other metazoans or gene loss. While SP, EGR and Klumpfuss were only detected in metazoans, KLF, WT1, and Huckebein are present in nonmetazoan holozoans. Of the seven metazoan KLF groups, only KLFG, represented by KLF15 in human, was found in nonmetazoans. In addition, two nonmetazoan groups of KLFs are present in Choanoflagellatea and Filasterea. WT1 could be evolutionarily the earliest among these GC/GT-box-binding families due to its sole presence in Ichthyosporea.

Original languageEnglish (US)
Article number40812
Pages (from-to)91-99
Number of pages9
JournalGene
Volume573
Issue number1
DOIs
StatePublished - Nov 15 2015

Fingerprint

Wilms Tumor
Growth
Proteins
Ctenophora
Mesomycetozoea
Placozoa
GC Rich Sequence
Cnidaria
CYS2-HIS2 Zinc Fingers
Porifera
Protein C
Transcriptome
Vertebrates
Siblings
Mammals
Fishes
Cell Death
Transcription Factors
Genome

Keywords

  • C2H2 zinc fingers
  • EGR
  • Huckebein
  • Klumpfuss
  • SP/KLF
  • WT1

ASJC Scopus subject areas

  • Genetics

Cite this

C2H2 zinc finger proteins of the SP/KLF, Wilms tumor, EGR, Huckebein, and Klumpfuss families in metazoans and beyond. / Pei, Jimin; Grishin, Nick V.

In: Gene, Vol. 573, No. 1, 40812, 15.11.2015, p. 91-99.

Research output: Contribution to journalArticle

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abstract = "Specificity proteins (SPs) and Kr{\"u}ppel-Like Factors (KLFs) are C2H2-type zinc finger transcription factors that play essential roles in differentiation, development, proliferation and cell death. SP/KLF proteins, similarly to Wilms tumor protein 1 (WT1), Early Growth Response (EGR), Huckebein, and Klumpfuss, prefer to bind GC-rich sequences such as GC-box and CACCC-box (GT-box). We searched various genomes and transcriptomes of metazoans and single-cell holozoans for members of these families. Seven groups of KLFs (KLFA-G) and three groups of SPs (SPA-C) were identified in the three lineages of Bilateria (Deuterostomia, Ecdysozoa, and Lophotrochozoa). The last ancestor of jawed vertebrates was inferred to have at least 18 KLFs (group A: KLF1/2/4/17, group B: KLF3/8/12; group C: KLF5/5l; group D: KLF6/7; group E: KLF9/13/16; group F: KLF10/KLF11; group G: KLF15/15l) and 10 SPs (group A: SP1/2/3/4; group B: SP5/5l; group C: SP6/7/8/9), since they were found in both cartilaginous and boned fishes. Placental mammals have added KLF14 (group E) and KLF18 (group A), and lost KLF5l (KLF5-like) and KLF15l (KLF15-like). Multiple KLF members were found in basal metazoans (Ctenophora, Porifera, Placozoa, and Cnidaria). Ctenophora has the least number of KLFs and no SPs, which could be attributed to its proposed sister group relationship to other metazoans or gene loss. While SP, EGR and Klumpfuss were only detected in metazoans, KLF, WT1, and Huckebein are present in nonmetazoan holozoans. Of the seven metazoan KLF groups, only KLFG, represented by KLF15 in human, was found in nonmetazoans. In addition, two nonmetazoan groups of KLFs are present in Choanoflagellatea and Filasterea. WT1 could be evolutionarily the earliest among these GC/GT-box-binding families due to its sole presence in Ichthyosporea.",
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AB - Specificity proteins (SPs) and Krüppel-Like Factors (KLFs) are C2H2-type zinc finger transcription factors that play essential roles in differentiation, development, proliferation and cell death. SP/KLF proteins, similarly to Wilms tumor protein 1 (WT1), Early Growth Response (EGR), Huckebein, and Klumpfuss, prefer to bind GC-rich sequences such as GC-box and CACCC-box (GT-box). We searched various genomes and transcriptomes of metazoans and single-cell holozoans for members of these families. Seven groups of KLFs (KLFA-G) and three groups of SPs (SPA-C) were identified in the three lineages of Bilateria (Deuterostomia, Ecdysozoa, and Lophotrochozoa). The last ancestor of jawed vertebrates was inferred to have at least 18 KLFs (group A: KLF1/2/4/17, group B: KLF3/8/12; group C: KLF5/5l; group D: KLF6/7; group E: KLF9/13/16; group F: KLF10/KLF11; group G: KLF15/15l) and 10 SPs (group A: SP1/2/3/4; group B: SP5/5l; group C: SP6/7/8/9), since they were found in both cartilaginous and boned fishes. Placental mammals have added KLF14 (group E) and KLF18 (group A), and lost KLF5l (KLF5-like) and KLF15l (KLF15-like). Multiple KLF members were found in basal metazoans (Ctenophora, Porifera, Placozoa, and Cnidaria). Ctenophora has the least number of KLFs and no SPs, which could be attributed to its proposed sister group relationship to other metazoans or gene loss. While SP, EGR and Klumpfuss were only detected in metazoans, KLF, WT1, and Huckebein are present in nonmetazoan holozoans. Of the seven metazoan KLF groups, only KLFG, represented by KLF15 in human, was found in nonmetazoans. In addition, two nonmetazoan groups of KLFs are present in Choanoflagellatea and Filasterea. WT1 could be evolutionarily the earliest among these GC/GT-box-binding families due to its sole presence in Ichthyosporea.

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