The HMGB protein gene family in zebrafish: Evolution and embryonic expression patterns

doi:10.1016/j.gep.2010.08.006

Gene Expression Patterns

Volume 11, Issues 1–2, January–February 2011, Pages 3-11

https://doi.org/10.1016/j.gep.2010.08.006 Get rights and content

Abstract

The High-Mobility Group Box (HMGB) proteins are highly abundant proteins with both nuclear and extracellular roles in key biological processes. In mammals, three family members are present: HMGB1, HMGB2 and HMGB3. We characterized the HMGB family in zebrafish and report a detailed phylogenetic analysis of HMGB proteins. The B1, B2, and B3 subfamilies are present in cartilaginous fish, bony fish, and tetrapods, while jawless fish sequences emerge as basal to the gene family expansion. Two co-orthologs of each mammalian HMGB gene are present in zebrafish. All six zebrafish hmgb genes are maternally expressed, but huge differences in expression levels exist during embryonic development. The hmgb2a/hmgb2b genes are the most highly expressed, while hmgb3b is expressed at the lowest level. Remarkably, hmgb3 genes are not present in fugu, medaka, Tetraodon and stickleback. Our analysis highlights substantial overlaps, but also subtle differences and specificities in the expression patterns of the zebrafish hmgb genes.

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

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Citation 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.
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¹: Present address: Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.

View full text

The HMGB protein gene family in zebrafish: Evolution and embryonic expression patterns

Abstract

Section snippets

Results and discussion

Zebrafish husbandry

Identification and analysis of hmgb sequences

Acknowledgments

Curr. Opin. Genet. Dev.

Am. J. Hum. Genet.

Trends Biochem. Sci.

Genomics

Blood

Blood

Trends Genet.

Gene

Gene

Gene

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.