OrfB

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Annotated Information

Function

It is generally believed that the CMS trait is associated with mitochondrial DNA (mtDNA) rearrangements, which result from the expressions of chimeric open reading frames (orf) or alterations in genomic structure and transcriptions patterns of mitochondrial genes .

Mutation

Experimental evidence for polymorphisms in orfB structural organization and mitochondrial transcript profiles of the orfB gene in the CMS-WA rice system. The sterile line orfB gene transcript profile was characterized by two transcripts of ~1.1 kb and ~0.7 kb, and one ~0.7 kb transcript was detected in the fertile lines. The ~1.1 kb transcript present in the sterile line remained unedited. However, in the presence of nuclear encoded restoration of fertility (Rf) gene(s) in fertile restored hybrid lines (APMS-6A × BR-1870; F1 generation), the ~1.1 kb orfB transcripts were fully edited. The editing of the orfB gene ~1.1 kb transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny of restored hybrid F1 plants. RFLPs were observed for the orfB gene in the mitochondrial genome between the sterile and the fertile lines,showing that mitochondrial orfB gene was present as a single copy with differential organization in the sterile and fertile lines. Mitochondrial RNA editing of the orfB transcript was assessed in the fertile rice line. Fourteen cDNA clones obtained from cDNA library of fertile rice line were sequenced. Determination of the orfB cDNA sequence from overlapping clones from the cDNA library showed four C→T conversions within the coding region relative to the orfB genomic sequence. Two editing events within the coding region affected the second position in a codon (200th and 443rd), and another event changed the first position (58th). These three editing events altered the coding properties of the affected triplets, which led to major changes in amino acids [Leu→Phe (20th), Ser→Leu (67th) and Pro→Leu (148th)]. Furthermore, editing at nucleotide position 200 in the coding region of orfB disrupted an XhoI restriction site (CTCGAG to CTTGAG). The fourth substitution was at the third position of a codon for leucine and was silent (Figure 4). Results showed that all four sites within the coding region were edited in all 14 clones. This indicated highly efficient and consistent mitochondrial editing for this transcript in the fertile rice line. (b) The sterile line orfB cDNA sequences were determined from overlapping clones of the cDNA library from the sterile rice line. Twelve orfB cDNA clones were completely sequenced. The size of the inserts ranged from 647 bp to 230 bp. Analysis of the clones revealed that they comprised sequences that overlapped with each other and were homologous to the nucleotide sequence of orfB cDNA from the fertile line (Figure 4). However, in contrast to the cDNA clones from the fertile line, unedited as well as edited cDNA clones were obtained from the sterile line. The edited clones exhibited identical editing to the cDNA clones in the fertile line. Interestingly, however, in the clone with the largest insert (6A25-11) editing was absent. Sequence analysis also indicated the insert contained a portion of the 5’ UTR region of the orfB gene, not detected in 0.7 kb orfB gene transcripts of the fertile lines. It was therefore inferred that the clone contained an insert originating from the long 1.1 kb transcript of the orfB gene. Furthermore, an additional interesting clone (6A21-61) of 230 bp was detected. It contained three unedited sites; unlike the other two clones that contained one unedited site out of four, normally found edited within the orfB gene coding sequence (CDS). abserving that some of the orfB gene transcripts in the sterile line remain unedited appeared significant.

Expression

OrfB gene is located at the downstream of mitochondrial nad2 gene in the CMS.The novel orfB gene had high similarity with YMF19 family protein.In many cases, CMS-associated genes or sequences were caused by rearrangements of mitochondrial genomes resulting in the birth of new orfs composed of fragments of other mitochondrial respiratory-related genes or non-coding sequences . Usually, such chimeric orfs were located at the flanking of mitochondrial respiratory/ATP synthesis-related genes and co-transcribed with these genes.

Labs working on this gene

• Advanced Laboratory for Plant Genetic Engineering (formerly IIT-BREF Biotek), Indian Institute of Technology, Kharagpur- 721302, India

References

<references>

and applications. Prog Bot 60:139–166

Gene Name	orfB
Description	ORFB protein
Version	GeneID:6450152
Length	468 bp
Definition	Oryza sativa Japonica Group orfB, Mitochondrion gene.
Source	Oryza sativa Japonica Group ORGANISM Oryza sativa Japonica Group Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP clade; Ehrhartoideae; Oryzeae; Oryza.
Chromosome	Mitochondrion
Location	Mitochondrion:53424..53891
Sequence Coding Region	53424..53891
Genome Context	<gbrowseImage3> name=NC_011033:53424..53891 source=Rice_Japonica_Mitochondrion preset=GeneLocation </gbrowseImage3>
Gene Structure (RNA Editing)	<gbrowseImage2> name=NC_011033:53424..53891 source=Rice_Japonica_Mitochondrion preset=GeneLocation </gbrowseImage2>
Protein Sequence	<aaseq>MPQLDKLTYFSQFFWLCLFFFSFYILLLNNNNGILGISRILKLRNQLLSHRGNKIRFKDPKNLEDILRKGFSTGLSYMYSSLSEVSQWCKTVDYLGKRRKITLISDFGEISGSRGMERQILYLISKSSYNTSSSRITCWKKIMLTHVLHGQGSII</aaseq>
Gene Sequence	<dnaseqindica>1..468#atgcctcaacttgataaattgacttatttctcacaattcttctggttatgccttttcctctttagtttttatattctcttattaaataataataatggaatacttggaattagcagaattctcaaactacggaaccaactgctttcgcaccgggggaacaagatccgtttcaaggaccctaagaatttggaagatatctcgagaaaaggttttagcaccggtctctcatatatgtactccagtttatccgaagtatcccaatggtgtaagaccgtcgactatttgggaaaaaggaggaaaatcactctgatctcagatttcggagaaataagtggctcacgaggaatggagagacagattctctatttgatctcgaagtcctcatataacacttcttccagtcggatcacttgttggaaaaaaataatgctcacacatgttccacacgggcaaggaagcataatctaa</dnaseqindica>
External Link(s)	NCBI Gene:orfB