The HMGB protein gene family in zebrafish: Evolution and embryonic expression patterns
Section snippets
Results and discussion
The High-Mobility Group Box (HMGB) proteins are abundant non-histone chromatin components implicated in major DNA transactions, such as transcription, recombination, and repair (Bianchi and Agresti, 2005, Bustin, 2001, Lange and Vasquez, 2009). HMGB proteins are highly mobile nuclear proteins that dynamically bind DNA and nucleoprotein complexes through their HMG boxes. These are L-shaped basic domains, that contact DNA through the minor groove and induce sharp DNA bending. HMGB1, the first
Zebrafish husbandry
Zebrafish of the wild-type AB line (obtained from Wilson lab, University College London) were raised and maintained according to established techniques (Westerfield, 1993). Embryos used in whole-mount in situ hybridization were raised in 0.003% PTU (Sigma) to prevent pigmentation.
Identification and analysis of hmgb sequences
Zebrafish hmgb sequences were identified using mouse HMGB1, HMGB2, and HMGB3 protein sequences to query Danio rerio nucleotide collection/EST databases with the TBLASTN program. A predicted gene, identical to the zf
Acknowledgments
We would like to thank C. Lora-Lamia for advice on histological techniques, G. Brunetti for his help in fish husbandry. We also thank Sylvie Rétaux for sharing with us lamprey sequences before publication in databases, Matthieu Muffato and Hugues Roest Crollius for help with synteny analysis, Gavin Laird for discussions on zebrafish genome annotation. We acknowledge financial support from Italian Ministry of Education, University, and Research (MIUR-Cofin 2004 to M.B.), Fondazione Cariplo
References (42)
- et al.
HMG proteins: dynamic players in gene regulation and differentiation
Curr. Opin. Genet. Dev.
(2005) - et al.
Flexing DNA: HMG-box proteins and their partners
Am. J. Hum. Genet.
(1998) Revised nomenclature for high mobility group (HMG) chromosomal proteins
Trends Biochem. Sci.
(2001)- et al.
The I.M.A.G.E. consortium: an integrated molecular analysis of genomes and their expression
Genomics
(1996) - et al.
Hmgb3 deficiency deregulates proliferation and differentiation of common lymphoid and myeloid progenitors
Blood
(2005) - et al.
Hmgb3: an HMG-box family member expressed in primitive hematopoietic cells that inhibits myeloid and B-cell differentiation
Blood
(2003) - et al.
Reciprocal gene loss between tetraodon and zebrafish after whole genome duplication in their ancestor
Trends Genet.
(2007) - et al.
The evolution of High Mobility Group Box (HMGB) chromatin proteins in multicellular animals
Gene
(2007) - et al.
Cloning and analysis of an HMG gene from the lamprey Lampetra fluviatilis: gene duplication in vertebrate evolution
Gene
(1997) - et al.
CDNA sequence and structure of a trout HMG-2 gene. Evidence for a trout-specific 3′-untranslated region
Gene
(1995)
Hmg4, a new member of the Hmg1/2 gene family
Genomics
ProtTest: selection of best-fit models of protein evolution
Bioinformatics
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Nucleic Acids Res.
HMGB1 loves company
J. Leukoc. Biol.
The lack of chromosomal protein Hmg1 does not disrupt cell growth but causes lethal hypoglycaemia in newborn mice
Nat. Genet.
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
Mol. Biol. Evol.
HMGB2 protein from the marine sponge Suberites domuncula
Food Technol. Biotechnol.
Fish as models for environmental genomics
Nat. Rev. Genet.
Two rounds of whole genome duplication in the ancestral vertebrate
PLoS Biol.
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Nucleic Acids Res.
Analysis of lamprey and hagfish genes reveals a complex history of gene duplications during early vertebrate evolution
Mol. Biol. Evol.
Cited by (35)
Functional identification of two HMGB1 paralogues provides insights into autophagic machinery in teleost
2024, Fish and Shellfish ImmunologyDesign and functional characterization of Salmo salar TLR5 agonist peptides derived from high mobility group B1 acidic tail
2024, Fish and Shellfish ImmunologyMolecular cloning and functional characterization of HMGB1 and HMGB2 in large yellow croaker Larimichthys crocea
2022, Fish and Shellfish ImmunologyPfHMGB2 protects yellow catfish (Pelteobagrus fulvidraco) from bacterial infection by promoting phagocytosis and proliferation of PBL
2019, Fish and Shellfish ImmunologyTranscriptomic analysis reveals dose-dependent modes of action of benzo(a)pyrene in polar cod (Boreogadus saida)
2019, Science of the Total EnvironmentCitation Excerpt :Transcriptomic analysis further revealed that exposure to both Low and High BaP affected DEGs related to DNA damage in polar cod, however, in different manners. Exposure to Low BaP mainly caused down-regulation of DEGs involved in DNA ligation during base-excision repair, such as high-mobility group protein B2 (hmgb2b), a key gene involved in DNA transcription, recombination, and repair in fish (Moleri et al., 2011). Similar to the down-regulation of AOX genes found in this study, the suppression of DNA repair genes may likely indicate reduced demand for DNA damage responses, possibly due to the suppression of oxidative stress as a result of reduced metabolic activities and ROS formation.
- 1
Present address: Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.