Why so Complex? The Intricacy of Genome Structure and Gene Expression, Associated with Angiosperm Mitochondria, May Relate to the Regulation of Embryo Quiescence or Dormancy—Intrinsic Blocks to Early Plant Life

Mitochondria play key roles in cellular-energy metabolism and are vital for plant-life, such as for successful germination and early-seedling establishment. Most mitochondria contain their own genetic system (mtDNA, mitogenome), with an intrinsic protein-synthesis machinery. Although the challenges of maintaining prokaryotic-type structures and functions are common to Eukarya, land plants possess some of the most complex organelle composition of all known organisms. Angiosperms mtDNAs are characteristically the largest and least gene-dense among the eukaryotes. They often contain highly-variable intergenic regions of endogenous or foreign origins and undergo frequent recombination events, which result in different mtDNA configurations, even between closely-related species. The expression of the mitogenome in angiosperms involves extensive mtRNA processing steps, including numerous editing and splicing events. Why do land-plant’s mitochondria have to be so complex? The answer to this remains a matter of speculation. We propose that this complexity may have arisen throughout the terrestrialization of plants, as a means to control embryonic mitochondrial functions —a critical adaptive trait to optimize seed germination. The unique characteristics of plant mtDNA may play pivotal roles in the nuclear-regulation of organellar biogenesis and metabolism, possibly to control embryos quiescence or dormancy, essential determinants for the establishment of viable plantlets that can survive post-germination.

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Seed coating reduces respiration losses and affects sugar metabolism during germination and early seedling growth in cereals

Functional Plant Biology ◽

10.1071/fp14142 ◽

2015 ◽

Vol 42 (2) ◽

pp. 209 ◽

Cited By ~ 8

Author(s):

Linda Gorim ◽

Folkard Asch

Keyword(s):

Seedling Growth ◽

Sucrose Synthase ◽

Sugar Metabolism ◽

Seedling Vigour ◽

Early Seedling Growth ◽

Plant Life ◽

Early Seedling ◽

Successful Establishment ◽

The Relationship ◽

Seed Coats

Seed germination and the successful establishment of young seedlings is an important aspect of plant life. Seed coats are used to improve stand establishment and early seedling vigour. Seedlings growing from hydro-absorber coated barley, rye and wheat with coat-shares greater than 75% of the average seed have been shown to promote better seedling growth compared with those seedlings growing from uncoated seeds. We investigated how and why these seedlings performed better by analysing the proportion of grain reserves mobilised for growth and respiration as well as how both sucrose and glucose available in the embryo translated into seedling growth in the presence or absence of seed coats containing hydro-absorber gel. We found that mobilisation efficiency was higher, resulting in higher biomass in these cereals when they were coated. The relationship between sucrose and glucose available to the seedling as well as its correlation with early seedling growth indicate a switch in the enzymatic cleavage of embryonic sucrose from invertase to sucrose synthase. This in turn indicates that in coated seeds, embryonic tissue must be hypoxic leading to a more efficient use of glucose and thus reduced respiration losses during germination.

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ARABIDOPSIS NITRATE REGULATED 1 acts as a negative modulator of seed germination by activating ABI3 expression

10.1101/708222 ◽

2019 ◽

Author(s):

Jia-Hui Lin ◽

Lin-Hui Yu ◽

Cheng-Bin Xiang

Keyword(s):

Seed Germination ◽

Chromatin Immunoprecipitation ◽

Mads Box ◽

Knockout Mutant ◽

Plant Life ◽

Similar Expression Pattern ◽

Early Seedling ◽

Safeguard Mechanism ◽

Early Seedling Development ◽

Salt And Osmotic Stress

ABSTRACTSeed germination is a crucial transition point in plant life and is tightly regulated by environmental conditions through the coordination of two phytohormones, gibberellin and abscisic acid (ABA). To avoid unfavorable conditions, plants have evolved safeguard mechanisms for seed germination. Here, we report a novel function of the Arabidopsis MADS-box transcription factor ARABIDOPSIS NITRATE REGULATED 1 (ANR1) in seed germination. ANR1 knockout mutant is insensitive to ABA, salt, and osmotic stress during the seed germination and early seedling development stages, whereas ANR1-overexpressing lines are hypersensitive. ANR1 is responsive to ABA and abiotic stresses and upregulates the expression of ABI3 to suppress seed germination. ANR1 and ABI3 have similar expression pattern during seed germination. Genetically, ABI3 acts downstream of ANR1. Chromatin immunoprecipitation and yeast-one-hybrid assays showed that ANR1 could bind to the ABI3 promoter to regulate its expression. In addition, ANR1 acts synergistically with AGL21 to suppress seed germination in response to ABA as evidenced by anr1 agl21 double mutant. Taken together, our results demonstrate that the ANR1 plays an important role in regulating seed germination and early post-germination growth. ANR1 and AGL21 together constitutes a safeguard mechanism for seed germination to avoid unfavorable conditions.

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IDENTIFICATION OF A GENE REGULATING THE TISSUE EXPRESSION OF A PHOSPHOGLUCOMUTASE LOCUS IN RAINBOW TROUT

Genetics ◽

10.1093/genetics/102.2.259 ◽

1982 ◽

Vol 102 (2) ◽

pp. 259-268

Author(s):

Fred W Allendorf ◽

Kathy L Knudsen ◽

Stevan R Phelps

Keyword(s):

Rainbow Trout ◽

Regulatory Gene ◽

Fold Increase ◽

Genetic System ◽

Tissue Expression ◽

Salmo Gairdneri ◽

Closely Related Species ◽

Control Of Gene Expression ◽

Normal Expression ◽

Additive Inheritance

ABSTRACT Nine percent of the rainbow trout (Salmo gairdneri) from a hatchery source have a greater than 100-fold increase in expression of a phosphoglucomutase (PGM) locus, Pgm1, in the liver but have normal expression of this locus in other tissues. The results of genetic crosses are consistent with a single regulatory gene with additive inheritance being responsible for the differences in the amount of PGM activity in the liver.—The allele responsible for the expression of Pgm1 in the liver is apparently a recent mutation. This is supported by its restricted distribution in rainbow trout and the absence of liver Pgm1 expression in closely related species. This genetic system is valuable for future analysis of the control of gene expression and in determining the relative evolutionary importance of genetic variation at structural and regulatory genes.

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CCA-Addition Gone Wild: Unusual Occurrence and Phylogeny of Four Different tRNA Nucleotidyltransferases in Acanthamoeba castellanii

Molecular Biology and Evolution ◽

10.1093/molbev/msaa270 ◽

2020 ◽

Author(s):

Lieselotte Erber ◽

Heike Betat ◽

Mario Mörl

Keyword(s):

Single Gene ◽

Acanthamoeba Castellanii ◽

Bioinformatic Analysis ◽

Protein Synthesis Machinery ◽

Mitochondrial Target ◽

Bona Fide ◽

Unusual Occurrence ◽

Eukaryotic Organisms ◽

Processing Steps

Abstract tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba castellanii, a highly unusual evolution of some of these processing steps was identified that are based on unconventional RNA polymerase activities. In this context, we investigated the synthesis of the 3′-terminal CCA-end that is added posttranscriptionally by a specialized polymerase, the tRNA nucleotidyltransferase (CCA-adding enzyme). The majority of eukaryotic organisms carry only a single gene for a CCA-adding enzyme that acts on both the cytosolic and the mitochondrial tRNA pool. In a bioinformatic analysis of the genome of this organism, we identified a surprising multitude of genes for enzymes that contain the active site signature of eukaryotic/eubacterial tRNA nucleotidyltransferases. In vitro activity analyses of these enzymes revealed that two proteins represent bona fide CCA-adding enzymes, one of them carrying an N-terminal sequence corresponding to a putative mitochondrial target signal. The other enzymes have restricted activities and represent CC- and A-adding enzymes, respectively. The A-adding enzyme is of particular interest, as its sequence is closely related to corresponding enzymes from Proteobacteria, indicating a horizontal gene transfer. Interestingly, this unusual diversity of nucleotidyltransferase genes is not restricted to Acanthamoeba castellanii but is also present in other members of the Acanthamoeba genus, indicating an ancient evolutionary trait.

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Transcriptional Paradigms in Mammalian Mitochondrial Biogenesis and Function

Physiological Reviews ◽

10.1152/physrev.00025.2007 ◽

2008 ◽

Vol 88 (2) ◽

pp. 611-638 ◽

Cited By ~ 919

Author(s):

Richard C. Scarpulla

Keyword(s):

Transcription Factors ◽

Mitochondrial Biogenesis ◽

Target Genes ◽

Protein Import ◽

Genetic System ◽

Environmental Signals ◽

Mitochondrial Functions ◽

Promoter Recognition ◽

Energy Deprivation ◽

And Function

Mitochondria contain their own genetic system and undergo a unique mode of cytoplasmic inheritance. Each organelle has multiple copies of a covalently closed circular DNA genome (mtDNA). The entire protein coding capacity of mtDNA is devoted to the synthesis of 13 essential subunits of the inner membrane complexes of the respiratory apparatus. Thus the majority of respiratory proteins and all of the other gene products necessary for the myriad mitochondrial functions are derived from nuclear genes. Transcription of mtDNA requires a small number of nucleus-encoded proteins including a single RNA polymerase (POLRMT), auxiliary factors necessary for promoter recognition (TFB1M, TFB2M) and activation (Tfam), and a termination factor (mTERF). This relatively simple system can account for the bidirectional transcription of mtDNA from divergent promoters and key termination events controlling the rRNA/mRNA ratio. Nucleomitochondrial interactions depend on the interplay between transcription factors (NRF-1, NRF-2, PPARα, ERRα, Sp1, and others) and members of the PGC-1 family of regulated coactivators (PGC-1α, PGC-1β, and PRC). The transcription factors target genes that specify the respiratory chain, the mitochondrial transcription, translation and replication machinery, and protein import and assembly apparatus among others. These factors are in turn activated directly or indirectly by PGC-1 family coactivators whose differential expression is controlled by an array of environmental signals including temperature, energy deprivation, and availability of nutrients and growth factors. These transcriptional paradigms provide a basic framework for understanding the integration of mitochondrial biogenesis and function with signaling events that dictate cell- and tissue-specific energetic properties.

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Polyploidy and apomixis in the Casuarina distyla species group

Australian Journal of Botany ◽

10.1071/bt9590238 ◽

1959 ◽

Vol 7 (3) ◽

pp. 238 ◽

Cited By ~ 8

Author(s):

BA Barlow

Keyword(s):

Breeding System ◽

Related Species ◽

Genetic System ◽

Species Group ◽

The Other ◽

Diploid Population ◽

Closely Related Species ◽

Triploid Plant

In the Casuarina distyla species group, which includes 13 closely related species, sexual tetraploid forms have been recorded in nine species and apomictic triploids in four. These forms are probably autopolyploids. The triploid apomiots are presumably diplosporous and parthenogenetic, and in two species are pseudogamous, but not in the other two. It is suggested that a transition from the former to the latter breeding system would follow elimination of the need for pseudogamy. A hypothesis is presented that polyploidy and apomixis have arisen together within the species through establishment in a diploid population of a triploid plant which is diplosporous and parthenogenetic. The genetic system involved probably spread through the group during the evolution of the species, giving them a potential for this kind of development.

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High global diversity of cycloviruses amongst dragonflies

Journal of General Virology ◽

10.1099/vir.0.052654-0 ◽

2013 ◽

Vol 94 (8) ◽

pp. 1827-1840 ◽

Cited By ~ 45

Author(s):

Anisha Dayaram ◽

Kristen A. Potter ◽

Angela B. Moline ◽

Dana Drake Rosenstein ◽

Milen Marinov ◽

...

Keyword(s):

Genomic Sequence ◽

Sequence Data ◽

Genome Structure ◽

Sister Group ◽

Regulatory Elements ◽

Intergenic Regions ◽

The Usa ◽

Circular Ssdna ◽

Insect Populations ◽

Ssdna Viruses

Members of the family Circoviridae, specifically the genus Circovirus, were thought to infect only vertebrates; however, members of a sister group under the same family, the proposed genus Cyclovirus, have been detected recently in insects. In an effort to explore the diversity of cycloviruses and better understand the evolution of these novel ssDNA viruses, here we present five cycloviruses isolated from three dragonfly species (Orthetrum sabina, Xanthocnemis zealandica and Rhionaeschna multicolor) collected in Australia, New Zealand and the USA, respectively. The genomes of these five viruses share similar genome structure to other cycloviruses, with a circular ~1.7 kb genome and two major bidirectionally transcribed ORFs. The genomic sequence data gathered during this study were combined with all cyclovirus genomes available in public databases to identify conserved motifs and regulatory elements in the intergenic regions, as well as determine diversity and recombinant regions within their genomes. The genomes reported here represent four different cyclovirus species, three of which are novel. Our results confirm that cycloviruses circulate widely in winged-insect populations; in eight different cyclovirus species identified in dragonflies to date, some of these exhibit a broad geographical distribution. Recombination analysis revealed both intra- and inter-species recombination events amongst cycloviruses, including genomes recovered from disparate sources (e.g. goat meat and human faeces). Similar to other well-characterized circular ssDNA viruses, recombination may play an important role in cyclovirus evolution.

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Impact of transposable elements on genome structure and evolution in bread wheat

10.1101/363192 ◽

2018 ◽

Cited By ~ 2

Author(s):

Thomas Wicker ◽

Heidrun Gundlach ◽

Manuel Spannagl ◽

Cristobal Uauy ◽

Philippa Borrill ◽

...

Keyword(s):

Transposable Elements ◽

Bread Wheat ◽

Genome Structure ◽

Reference Sequence ◽

Structural Level ◽

Gene Promoters ◽

Genome Wide ◽

Intergenic Regions ◽

History Of ◽

First Time

AbstractBackgroundTransposable elements (TEs) are ubiquitous components of genomes and they are the main contributors to genome evolution. The reference sequence of the hexaploid bread wheat (Triticum aestivum L.) genome enabled for the first time a comprehensive genome-wide view of the dynamics of TEs that have massively proliferated in the A, B, and D subgenomes.ResultsTEs represent 85% of the genome. We traced back TE amplification dynamics in the evolutionary history of wheat and did not find large bursts in the wake of either the tetra- or the hexaploidization. Despite the massive turnover of TEs since A, B, and D diverged, 76% of TE families are present in similar proportions in the three subgenomes. Moreover, spacing between homeologous genes was also conserved. TE content around genes is very different from the TE space comprising large intergenic regions and families that are enriched or depleted from gene promoters are the same in the three subgenomes.ConclusionsThe chromosome-scale assembly of the wheat genome provided an unprecedented genome-wide view of the organization and impact of TEs in such a complex genome. Our results suggest that TEs play a role at the structural level and that the overall chromatin structure is likely under selection pressure.

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Comparative analysis of Streptococcus genomes

10.1101/447938 ◽

2018 ◽

Cited By ~ 1

Author(s):

Pavel V Shelyakin ◽

Olga O Bochkareva ◽

Anna A Karan ◽

Mikhail S Gelfand

Keyword(s):

Genome Evolution ◽

Genome Structure ◽

Genomic Analysis ◽

Single Copy ◽

Strong Impact ◽

Nucleotide Substitutions ◽

Pan Genome ◽

Conserved Genes ◽

Intergenic Regions ◽

Multiple Strains

AbstractBackgroundGenome sequencing of multiple strains demonstrated high variability in gene content even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome, that is, the complete set of genes observed in a given species or a higher level taxon. Here we analysed the pan-genome structure and the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.ResultsFractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.About 7% of single-copy periphery genes have been found in different syntenic regions. More than a half of these genes are rare in all Streptococcus species; others are rare in at least one species. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are candidates for horizontal transfer between species.An inversion of length 15 kB found in four independent branches of S. pneumoniae has breakpoints formed by genes encoding a surface antigen protein (PhtD). The observed parallelism may indicate the action of an antigen variation mechanism.ConclusionsMembers of the genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, understanding of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines.

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Plant super-barcode: a case study on genome-based identification for closely related species of Fritillaria

Chinese Medicine ◽

10.1186/s13020-021-00460-z ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Lan Wu ◽

Mingli Wu ◽

Ning Cui ◽

Li Xiang ◽

Ying Li ◽

...

Keyword(s):

Medicinal Plants ◽

Related Species ◽

Genome Structure ◽

Dna Barcode ◽

Intergenic Spacer ◽

Discrimination Power ◽

Closely Related Species ◽

Wide Range ◽

High Discrimination ◽

Cp Genome

Abstract Background Although molecular analysis offers a wide range of options for species identification, a universal methodology for classifying and distinguishing closely related species remains elusive. This study validated the effectiveness of utilizing the entire chloroplast (cp) genome as a super-barcode to help identify and classify closely related species. Methods We here compared 26 complete cp genomes of ten Fritillaria species including 18 new sequences sequenced in this study. Each species had repeats and the cp genomes were used as a whole DNA barcode to test whether they can distinguish Fritillaria species. Results The cp genomes of Fritillaria medicinal plants were conserved in genome structure, gene type, and gene content. Comparison analysis of the Fritillaria cp genomes revealed that the intergenic spacer regions were highly divergent compared with other regions. By constructing the phylogenetic tree by the maximum likelihood and maximum parsimony methods, we found that the entire cp genome showed a high discrimination power for Fritillaria species with individuals of each species in a monophyletic clade. These results indicate that cp genome can be used to effectively differentiate medicinal plants from the genus Fritillaria at the species level. Conclusions This study implies that cp genome can provide distinguishing differences to help identify closely related Fritillaria species, and has the potential to be served as a universal super-barcode for plant identification.

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