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Review
. 2014 Oct 27:3:253.
doi: 10.12688/f1000research.5530.2. eCollection 2014.

Rice ( Oryza) hemoglobins

Affiliations
Review

Rice ( Oryza) hemoglobins

Raúl Arredondo-Peter et al. F1000Res. .

Abstract

Hemoglobins (Hbs) corresponding to non-symbiotic (nsHb) and truncated (tHb) Hbs have been identified in rice ( Oryza). This review discusses the major findings from the current studies on rice Hbs. At the molecular level, a family of the nshb genes, consisting of hb1, hb2, hb3, hb4 and hb5, and a single copy of the thb gene exist in Oryza sativa var. indica and O. sativa var. japonica, Hb transcripts coexist in rice organs and Hb polypeptides exist in rice embryonic and vegetative organs and in the cytoplasm of differentiating cells. At the structural level, the crystal structure of rice Hb1 has been elucidated, and the structures of the other rice Hbs have been modeled. Kinetic analysis indicated that rice Hb1 and 2, and possibly rice Hb3 and 4, exhibit a very high affinity for O 2, whereas rice Hb5 and tHb possibly exhibit a low to moderate affinity for O 2. Based on the accumulated information on the properties of rice Hbs and data from the analysis of other plant and non-plant Hbs, it is likely that Hbs play a variety of roles in rice organs, including O 2-transport, O 2-sensing, NO-scavenging and redox-signaling. From an evolutionary perspective, an outline for the evolution of rice Hbs is available. Rice nshb and thb genes vertically evolved through different lineages, rice nsHbs evolved into clade I and clade II lineages and rice nshbs and thbs evolved under the effect of neutral selection. This review also reveals lacunae in our ability to completely understand rice Hbs. Primary lacunae are the absence of experimental information about the precise functions of rice Hbs, the properties of modeled rice Hbs and the cis-elements and trans-acting factors that regulate the expression of rice hb genes, and the partial understanding of the evolution of rice Hbs.

Keywords: Evolution; function; gene expression; non-symbiotic; structure; symbiotic; truncated.

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Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Early (1991) detection of rice, maize, sorghum and wheat hb-like sequences by dot-blot hybridization (R. Arredondo-Peter, unpublished results).
Approximately 20 μg of undigested total DNA was used as template and a consensus oligonucleotide for legume and non-legume plant Hbs was used as probe. Sequence of the consensus probe was 5´-GTA GCC TAT GAT GAA TTG GCA GCT GCA ATT AAG-3´. The probe was labeled by nick translation with Biotin-dATP using a Bionick labeling system (Gibco BRL). The membrane was prehybridized with SSC 2× for 4h at 42°C, hybridized overnight at the same temperature, washed at high stringency (SSC 2×/SDS 0.1% for 3 min at room temperature, SSC 0.2×/SDS 0.1% for 15 min at room temperature and SSC 0.16×/SDS 0.1% for 15 min at 65°C) and incubated with the streptavidin-alkaline phosphatase conjugate and the BCIP/NBT mix to develop color. Animal (salmon sperm and calf thymus) and legume DNAs were included as negative and positive controls, respectively.
Figure 2.
Figure 2.. Localization of hbs in the O. sativa chromosomes (A) and mapping of hb genes into the O. sativa genome (B).
The hb genes were localized in the rice chromosomes by BlastN analysis using the rice ( O. sativa) genome resource from the GenBank database as template and the sequence for the rice hb1, hb3 and hb4 (GenBank accession number AF335504), hb2 and hb5 (GenBank accession numbers AF335503 and EF061459, respectively) and thb (GenBank accession number NM_001064507) genes as probes. The hb (black boxes) and flanking (gray boxes) genes were mapped into 50 kb fragments of the O. sativa genome by BlastN2.2.26+ analysis using the Phytozome V9.1 server ( www.phytozome.org) and the above hb sequences as probes. Arrows indicate the transcription orientation. Information for each gene corresponds to predicted protein (following the Phytozome nomenclature), locus name in the O. sativa genome and position at the O. sativa chromosome. Gene sizes and distance between genes are not shown at scale. Pltd, chloroplast chromosome; MT, mitochondrial chromosome.
Figure 3.
Figure 3.. Sequence alignment of rice Hbs.
( A) Sequence alignment of rice nsHbs. Note the 11 amino acids deletion in rice Hb5 at position 75–85. Modified from Garrocho-Villegas et al. . ( B) Sequence alignment of rice and Arabidopsis (GenBank accession number AAK55409) tHbs. Distal and proximal His in rice nsHbs (H79 and H114, respectively) and proximal His (H100) and proposed distal Tyr/Tre (Y46/W113) in Arabidopsis and rice tHbs and conserved amino acids are shown with black and gray background, respectively. Helices are indicated with letters A to H based on the crystal structure of rice Hb1 in rice nsHbs and on the crystal structure of Arabidopsis tHb in rice tHb. Left- and right-oriented arrows within a black circle in the rice and Arabidopsis tHbs sequence alignment delimit the globin domain.
Figure 4.
Figure 4.. Crystal structure of rice Hb1 (PDB ID 1D8U) and predicted structure of rice tHb.
The tertiary structure of rice tHb was modeled using the automated mode of the I-Tasser server ( http://zhanglab.ccmb.med.umich.edu/I-TASSER/) and the crystal structure of the Thermobifida fusca tHb (PDB ID 2BMM) as the structural homologue. Model for the rice tHb is deposited in the Caspur Protein Model Database ( http://bioinformatics.cineca.it/PMDB/main.php) under the ID number PM0079484. Helices are indicated with letters A to H. Note the overlapping of helices A, E and F to helices B, G and H in (3/3-folding) rice Hb1, and overlapping of helices B and E to helices G and H in (2/2-folding) rice tHb. Heme prosthetic group is shown in dark green color and proximal and distal His are shown in light brown color.

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