Soybean leghemoglobin gene family: normal, pseudo, and truncated genes
01 Jul 1982-Proceedings of the National Academy of Sciences of the United States of America (National Academy of Sciences)-Vol. 79, Iss: 13, pp 4055-4059
TL;DR: Analysis of three Leghemoglobin genes in soybean revealed a truncated Lb gene showing homology with the last exon and the noncoding region at the 3' end of the two other Lb genes, which is not represented in any of the known Lb proteins.
Abstract: Leghemoglobin (Lb) genes in soybean represent a small family of closely related genes. Three Lb sequences isolated from a genomic library were analyzed at the nucleotide sequence level. A Lb gene present on an 11.5-kilobase (kb) EcoRI genomic fragment spans approximately 1,200 nucleotides and is interrupted at amino acid positions 32 to 33, 68 to 69, and 103 to 104. The intervening sequences, as well as the 5' and 3' flanking regions of this gene, contain the consensus sequences found in other eukaryotic genes. The length of the 5'-untranslated region is 49 bases as determined by nuclease S1 mapping. R-loop analysis of the DNA from the recombinant phage containing the 11.5-kb EcoRI genomic fragment showed that another Lb gene is located 2.5 kb away. The nucleotide sequence of the second gene showed that this gene is incomplete, containing only exons 3 and 4. The deduced amino acid sequence of this gene, although showing 76% homology with the corresponding region of the other Lb gene, is not represented in any of the known Lb proteins. Both genes are oriented in the same direction with respect to the coding strand. Analysis of the sequence present on a second genomic clone containing a 4.2-kb EcoRI fragment revealed a truncated Lb gene showing homology with the last exon and the noncoding region at the 3' end of the two other Lb genes.
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TL;DR: The sequence CCAGCCAUG (G) thus emerges as a consensus sequence for eukaryotic initiation sites, and the extent to which the ribosome binding site in a given mRNA matches the -1 to -5 consensus sequence varies.
Abstract: 5-Noncoding sequences have been tabulated for 211 messenger RNAs from higher eukaryotic cells. The 5'-proximal AUG triplet serves as the initiator codon in 95% of the mRNAs examined. The most conspicuous conserved feature is the presence of a purine (most often A) three nucleotides upstream from the AUG initiator codon; only 6 of the mRNAs in the survey have a pyrimidine in that position. There is a predominance of C in positions -1, -2, -4 and -5, just upstream from the initiator codon. The sequence CCAGCCAUG (G) thus emerges as a consensus sequence for eukaryotic initiation sites. The extent to which the ribosome binding site in a given mRNA matches the -1 to -5 consensus sequence varies: more than half of the mRNAs in the tabulation have 3 or 4 nucleotides in common with the CCACC consensus, but only ten mRNAs conform perfectly.
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TL;DR: This review concerns a dramatic association, one of the few that has been studied in detail: the nitrogen fixing symbiosis between certain plants and microbes Rhizobium bacteria stimulate leguminous plants to develop root nodules, which the bacteria infect and inhabit.
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Cites background from "Soybean leghemoglobin gene family: ..."
...Furthermore, the positions of two of the typical three Lb gene introns are very similar to the positions of the two hemoglobin gene introns (Brisson and Verma, 1982; Hyldig-Nielsen et al., 1982)....
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TL;DR: It is suggested that all the transcripts that gave rise to these pseudogenes were actually produced in the germ line cell, and that at least one processed pseudogene, the human DHFR psi 1, has been formed so recently that it is polymorphic.
Abstract: The processed pseudogenes reported to date fall into three categories: those that are a complete copy of the mRNA transcribed from the functional gene, those that are only a partial copy of the corresponding mRNA, and those that contain sequences in addition to those expected to be present in the mRNA. The general structural characteristics of these processed pseudogenes include the complete lack of intervening sequences found in the functional counterparts, a poly A tract at the 3' end, and direct repeats flanking the pseudogene sequence. In all the cases studied, these pseudogenes have been found to be on a different chromosome from their functional counterpart. These characteristics have led investigators to suggest that an RNA intermediate, in many cases the mRNA of the functional gene, is involved in the production of these pseudogenes. The mechanism by which processed pseudogenes arose involves the integration of the mRNA, or its cDNA copy, into a staggered chromosome break, followed by DNA synthesis and repair. I suggest that all the transcripts that gave rise to these pseudogenes were actually produced in the germ line cell. The transcripts that gave rise to the processed pseudogenes that are direct copies of the corresponding mRNA resulted from RNA polymerase II transcription of the functional counterpart. Pseudogenes that are not a direct copy of the corresponding mRNA may have resulted from RNA polymerase III transcription. If this is indeed the case, one need not postulate the involvement of retroviruses to explain the presence of processed pseudogenes corresponding to genes that are not expressed in the germ line. Following the integration event, processed pseudogenes can no longer be transcribed to produce the functional mRNA from which they arose. This inability to be transcribed by RNA polymerase II is not surprising considering that processed pseudogenes seem to be randomly integrated into the genome. Therefore, integration of a processed pseudogene such that RNA polymerase II transcriptional promoters are correctly positioned 5' to the resultant pseudogene is an unlikely event. The presence of processed pseudogenes seems peculiar to mammals. In fact, evolutionary studies indicate that processed pseudogenes are of relatively recent origin. In fact, at least one processed pseudogene, the human DHFR psi 1, has been formed so recently that it is polymorphic.
653 citations
TL;DR: The author revealed that Rhizobium Nitrogen Fixation Without Leghemoglobin could have been caused by either Nitrogenase Location and Oxygen Lability or Periplasmic Location of Bacteroid Oxidases.
Abstract: INTRODUCTION 444 LEGHEMOGLOBIN 445 Occurrence, Purification, Sequence Analysis 445 Biosynthesis and its Control; Genetic Origin 446 Maintenance, Turnover, and Degradation 448 Leghemoglobin Structure in Relation to Oxygen Reactivity 449 lntracellular Location of Leghemoglobin 451 LEGUME BACTEROIDS AND THE OXYGEN PARADOX 452 Nitrogenase Location and Oxygen Lability: Possible Protective Mechanisms ......... 452 Cytochrome Variation Among Free-living Rhizobia and Bacteroids 453 Periplasmic Location of Bacteroid Oxidases? 455 LEGHEMOGLOBIN A D RHIZOBIUM RESPIRATION EFFICIENCY 457 Oxygen Delivery and Other Possible Leghemoglobin Functions 457 The Soybean Symbiosis: Recognition of Efficient and Inefficient Phases of Bacteroid Respiration 459 Other Legume Symbioses: Evidence for Increasing Oxygen Tolerance 461 Respiration Substrate in Relation to Symbiotic Efficiency 466 Hemoglobin Nonlegume Symbioses 468 Rhizobium Nitrogen Fixation Without Leghemoglobin 470 CONCLUSIONS 471
632 citations
TL;DR: This chapter describes the origin and evolution of retroposons, a class of dispersed sequences in DNA which appear to have arisen during evolution by a particular mechanism of inserting RNA sequences into chromosomal DNA (retroposition).
Abstract: Publisher Summary This chapter describes the origin and evolution of retroposons. It deals with two of them which operate on very different timescales: (1) RNA splicing (particularly messenger RNA splicing), which is the excision of transcribed noncoding sequences from RNA during normal gene expression and (2) retroposition, which is the insertion of reverse-transcribed sequences from RNA back into the genome during evolution. RNA splicing was the first and most surprising discovery of eukaryotic molecular genetics. Retroposons are a class of dispersed sequences in DNA, which appear to have arisen during evolution by a particular mechanism of inserting RNA sequences into chromosomal DNA (retroposition). They include processed mRNA pseudogenes, snRNA pseudogenes, the highly repeated ALU sequences, and a variety of other sequences. They are entirely distinct from transposons and retroviruses. The chapter explains the splicing of ribosomal RNA, mitochondrial RNA, and chloroplast RNA.
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