Molecular Adaptation in Plant Hemoglobin, a Duplicated GeneInvolved in Plant�Bacteria Symbiosis (original) (raw)
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Two types of non-symbiotic hemoglobins (nsHbs) have been detected in angiosperms: nsHb-1 and nsHb-2. The origin of nshb-1 and nshb-2 prior to the monocot-dicot divergence was a major event in the evolution of land plant nsHbs. Because nshb-2 has not been detected in monocots, apparently only nshb-1 exists in monocots. Here, we report the phylogenetic analysis and in silico characterization of novel monocot (barley, Brachypodium, foxtail millet, maize, rice, sorghum, switchgrass, and wheat) nsHb sequences deposited in databases. Results suggest that only nshb-1 evolved within monocots; that nshb-1 duplicated early in the evolution of monocots, originating clade I and clade II nshbs (nshbs-I and nshbs-II, respectively); that nsHbs-I correspond to dicot nsHbs-1; and that nsHbs-II diversified into regular nsHbs-II, post-helix H-containing nsHbs-II, and 11 amino acids deletion-containing nsHbs-II. Molecular modeling showed that monocot nsHbs-II may fold into the myoglobin-fold and that Fe-heme is hexacoordinate in the predicted barley, Brachypodium, maize, and sorghum nsHb-II and pentacoordinate in the predicted foxtail millet, rice, and switchgrass nsHb-II.
The evolution of a plant globin gene family
Journal of Molecular Evolution, 1984
We have analyzed the sequences of Soybean leg, hemoglobin genes as an initial step toWard understanding their mode of evolution. Alignment of the sequences of plant globin genes with those of animals reveals that (i) based on the proportion of nucleotide substitutions that have occurred at the first, second, and third codon positions, the lime of divergence of plant and animal globin gene families appears to be extremely remote (be-tWeen 900 million and 1.4 billion years ago, if one assumes constancy of evolutionary rate in both the plant and animal lineages) and (ii) in addition to the normal regulatory sequences on the 5' end, an approximately 30-base-pair sequence, specific to globin genes, that surrounds the cap site is conserved between the plant and animal globin genes. ComParison of the leghemoglobin sequences with one another shows that (i) the relative amount of sequence divergence in various coding and noncoding regions is roughly similar to that found for animal globin genes and (ii) as in animal globin genes, the positions of insertions and deletions in the intervening sequences often coincide with the locations of direct repeats. Thus, the mode of evolution of the plant globin genes appears to resemble, in many Ways, that of their animal counterparts. We contrast the OVerall intergenic organization of the plant globin genes with that of animal genes, and discuss the Possibility of the concerted evolution of the leghemoglobin genes.
A single hemoglobin gene in Myrica gale retains both symbiotic and non-symbiotic specificity
Plant Molecular Biology, 2006
Here, a hemoglobin gene from the nitrogen-fixing actinorhizal plant Myrica gale was isolated, cloned and sequenced. The gene (MgHb) was a class I hemoglobin with strong sequence homology to non-symbiotic hemoglobin genes. MgHb is highly expressed in symbiotic root nodules, but transcripts and protein were also detected in leaves of M. gale. In Arabidopsis thaliana the MgHb promoter, linked to a β-glucuronidase coding region, directed expression in the vascular tissue, in shoot meristem and at root branch point - a pattern very similar to the combined expression pattern of the two non-symbiotic A. thaliana hemoglobin promoters AHb1 and AHb2. The results points to a symbiotic as well as a non-symbiotic specificity of MgHb similar to a hemoglobin gene identified in Parasponia andersonii, but different from the situation in Casuarina glauca - a close actinorhizal relative of M. gale.
Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern
BMC Evolutionary Biology, 2012
Background: The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages.
PLOS Computational Biology, 2021
The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant psbA gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of ...
Gene, 2007
Putative globins have been identified in 426 bacterial, 32 Archaeal and 67 eukaryote genomes. Among these sequences are the hitherto unsuspected presence of single domain sensor globins within Bacteria, Fungi, and a Euryarchaeote. Bayesian phylogenetic trees suggest that their occurrence in the latter two groups could be the result of lateral gene transfer from Bacteria. Iterated psiblast searches based on groups of globin sequences indicate that bacterial flavohemoglobins are closer to metazoan globins than to the other two lineages, the 2-over-2 globins and the globin-coupled sensors. Since Bacteria is the only kingdom to have all the subgroups of the three globin lineages, we propose a working model of globin evolution based on the assumption that all three lineages originated and evolved only in Bacteria. Although the 2-over-2 globins and the globin-coupled sensors recognize flavohemoglobins, there is little recognition between them. Thus, in the first stage of globin evolution, we favor a flavohemoglobin-like single domain protein as the ancestral globin. The next stage comprised the splitting off to single domain 2-over-2 and sensor-like globins, followed by the covalent addition of C-terminal domains resulting in the chimeric flavohemoglobins and globin-coupled sensors. The last stage encompassed the lateral gene transfers of some members of the three globin lineages to specific groups of Archaea and Eukaryotes.
Rapid evolution in plant–microbe interactions – a molecular genomics perspective
New Phytologist, 2019
Rapid (co-)evolution at multiple timescales is a hallmark of plant-microbe interactions. The mechanistic basis for the rapid evolution largely rests on the features of the genomes of the interacting partners involved. Here, we review recent insights in genomic characteristics and mechanisms that enable rapid evolution of both plants and phytopathogens. These comprise fresh insights in allelic series of matching pairs of resistance and avirulence genes, the generation of novel pathogen effectors, the recently recognized small RNA warfare, and genomic aspects of secondary metabolite biosynthesis. In addition, we discuss the putative contributions of permissive host environments, transcriptional plasticity and the role of ploidy on the interactions. We conclude that the means underlying the rapid evolution of plantmicrobe interactions are multifaceted and depend on the particular nature of each interaction.
Journal of Molecular Evolution
Two competing proposals about the degree to which selection affects codon usage of angiosperm chloroplast genes are examined. The first, based on observations that codon usage does not match expectations under the naïve assumption that base composition will be identical at all neutral sites, is that selection plays a significant role. The second is that codon usage is determined almost solely by mutation bias and drift, with selection influencing only one or two highly expressed genes, in particular psbA. First it is shown that, as a result of an influence of neighboring base composition on mutation dynamics, compositional biases are expected to be widely divergent at different sites in the absence of selection. The observed mutation properties are then used to predict expected neutral codon usage biases and to show that observed deviations from the naïve expectations are in fact expected given the context-dependent mutational dynamics. It is also shown that there is a match between...
A Phylogenetic study of Plant, Animal and Microbial Hemoglobin using MEGA
2014
Hemoglobin is an ancient class of molecule uniting almost all forms of life on this planet. Whenever the term hemoglobin is mentioned oxygen transport within erythrocytes in the circulatory system of blood is remembered. The name hemoglobin comes from the globular structure associated with heme prosthetic group which binds oxygen. It may be therefore surprising that non-blood containing plants also encode hemoglobin. (Gupta et al., 2011) What surprises most people is the ubiquitousness and varied functions of hemoglobins not just in the animal world. Plants use hemoglobins, as do fungi, protists and bacteria. The discovery of hemoglobins in virtually all kingdoms of organisms has shown that the ancestral gene for hemoglobin is ancient, and that hemoglobins can serve additional functions besides transport of oxygen ISSN: 2319-7706 Volume 3 Number 9 (2014) pp. 728-735 http://www.ijcmas.com