scholarly journals Organellar Introns in Fungi, Algae, and Plants

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2001
Author(s):  
Jigeesha Mukhopadhyay ◽  
Georg Hausner
Keyword(s):  
Gene Expression ◽  
Ribosomal Proteins ◽  
Heterologous Gene Expression ◽  
Group I Introns ◽  
Group Ii Introns ◽  
Homing Endonucleases ◽  
Organellar Genomes ◽  
Chloroplast Genomes ◽  
Group I ◽  
Group Ii

Introns are ubiquitous in eukaryotic genomes and have long been considered as ‘junk RNA’ but the huge energy expenditure in their transcription, removal, and degradation indicate that they may have functional significance and can offer evolutionary advantages. In fungi, plants and algae introns make a significant contribution to the size of the organellar genomes. Organellar introns are classified as catalytic self-splicing introns that can be categorized as either Group I or Group II introns. There are some biases, with Group I introns being more frequently encountered in fungal mitochondrial genomes, whereas among plants Group II introns dominate within the mitochondrial and chloroplast genomes. Organellar introns can encode a variety of proteins, such as maturases, homing endonucleases, reverse transcriptases, and, in some cases, ribosomal proteins, along with other novel open reading frames. Although organellar introns are viewed to be ribozymes, they do interact with various intron- or nuclear genome-encoded protein factors that assist in the intron RNA to fold into competent splicing structures, or facilitate the turn-over of intron RNAs to prevent reverse splicing. Organellar introns are also known to be involved in non-canonical splicing, such as backsplicing and trans-splicing which can result in novel splicing products or, in some instances, compensate for the fragmentation of genes by recombination events. In organellar genomes, Group I and II introns may exist in nested intronic arrangements, such as introns within introns, referred to as twintrons, where splicing of the external intron may be dependent on splicing of the internal intron. These nested or complex introns, with two or three-component intron modules, are being explored as platforms for alternative splicing and their possible function as molecular switches for modulating gene expression which could be potentially applied towards heterologous gene expression. This review explores recent findings on organellar Group I and II introns, focusing on splicing and mobility mechanisms aided by associated intron/nuclear encoded proteins and their potential roles in organellar gene expression and cross talk between nuclear and organellar genomes. Potential application for these types of elements in biotechnology are also discussed.

scholarly journals Chloroplast Genomes of the Green-Tide Forming Alga Ulva compressa: Comparative Chloroplast Genomics in the Genus Ulva (Ulvophyceae, Chlorophyta)

2021 ◽  
Vol 8 ◽  
Author(s):  
Feng Liu ◽  
James T. Melton
Keyword(s):  
Homing Endonuclease ◽  
Intergenic Spacer ◽  
Green Tide ◽  
Group I Introns ◽  
Intron Insertion ◽  
Chloroplast Genomes ◽  
Group I ◽  
Ulva Compressa ◽  
Insertion Sites ◽  
Group Ii

To understand the evolution of Ulva chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of Ulva compressa Linnaeus were sequenced and compared with the available Ulva cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of Ulva cpDNAs at intraspecific and interspecific levels were mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of non-coding intergenic spacer regions. Second, chloroplast genomes of U. compressa shared the same 100 conserved genes as other Ulva cpDNA, whereas Ulva flexuosa appears to be the only Ulva species with the minD gene retained in its cpDNA. Third, five types of group I introns, most of which carry a LAGLIDADG or GIY-YIG homing endonuclease, and three of group II introns, usually encoding a reverse transcriptase/maturase, were detected at 26 insertion sites of 14 host genes in the 23 Ulva chloroplast genomes, and many intron insertion-sites have been found for the first time in Chlorophyta. Fourth, one degenerate group II intron previously ignored has been detected in the infA genes of all Ulva species, but not in the closest neighbor, Pseudoneochloris marina, and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of Ulva species. Finally, the seven U. compressa cpDNAs represented a novel gene order which was different from that of other Ulva cpDNAs. The structure of Ulva chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.

scholarly journals Evolution of Antennapedia-Class Homeobox Genes

Genetics ◽  
1996 ◽  
Vol 142 (1) ◽  
pp. 295-303 ◽  
Author(s):  
Jianzhi Zhang ◽  
Masatoshi Nei
Keyword(s):  
Gene Expression ◽  
Homeobox Genes ◽  
Amino Acid Sequences ◽  
Gene Arrangement ◽  
Gene Duplications ◽  
Group I ◽  
Group 3 ◽  
Group Ii ◽  
Anterior Posterior

Antennapedia (Antp)-class homeobox genes are involved in the determination of pattern formation along the anterior-posterior axis of the animal embryo. A phylogenetic analysis of Antp-class homeodomains of the nematode, Drosophila, amphioxus, mouse, and human indicates that the 13 cognate group genes of this gene family can be divided into two major groups, i.e., groups I and II. Group I genes can further be divided into subgroups A (cognate groups 1–2), B (cognate group 3), and C (cognate groups 4–8), and group II genes can be divided into subgroups D (cognate groups 9–10) and E (cognate groups 11–13), though this classification is somewhat ambiguous. Evolutionary distances among different amino acid sequences suggest that the divergence between group I and group II genes occurred ∼1000 million years (MY) ago, and the five different subgroups were formed by ∼600 MY ago, probably before the divergence of Pseudocoelomates (e.g., nematodes) and Coelomates (e.g., insects and chordates). Our results show that the genes that are phylogenetically close are also closely located in the chromosome, suggesting that the colinearity between the gene expression and gene arrangement was generated by successive tandem gene duplications and that the gene arrangement has been maintained by some sort of selection.

57 DIETARY CLA SUPPLEMENTATION AFFECTS LUTEAL GENE EXPRESSION AND PERIPHERAL BLOOD PROGESTERONE CONCENTRATION IN CATTLE

2012 ◽  
Vol 24 (1) ◽  
pp. 140
Author(s):  
H. Stinshoff ◽  
E. Onnen-Lübben ◽  
S. Wilkening ◽  
A. Hanstedt ◽  
H. Bollwein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Corpus Luteum ◽  
Control Group ◽  
Progesterone Concentration ◽  
Blood Samples ◽  
Oral Supplementation ◽  
Group I ◽  
Pregnancy Status ◽  
Gene Transcripts ◽  
Group Ii

Shortly after parturition the metabolic situation of high-yielding dairy cows is often dominated by a negative energy balance. These effects affect the whole animal and may especially be detected in the reproductive tract, where they result in reduced fertility. An oral supplementation with dietary fats is often used to counteract by reducing milk fat content and, thus, supplying the individual animal with an increased amount of energy. The focus of the present study was to analyse the effects of an oral supplementation with conjugated linoleic acids (CLA) on corpus luteum (CL) function. Healthy Holstein-Friesian cows and heifers were randomly allocated to 2 treatment groups (Group 1: 50 g of CLA day–1 per animal, 2 heifers, 6 cows; Group 2: 100 g of CLA day–1 per animal, 2 heifers, 6 cows) and 1 control group (Ctl; 0 g of CLA day–1 per animal, 3 heifers, 4 cows). Feeding of the supplement began shortly after calving. After calving, all animals were subjected to a standard synchronisation protocol and experienced AI on Day 59 ± 3. Following AI, transvaginal biopsies of the corpus luteum were obtained of pregnant (Group I: n = 4; Group II: n = 4; Ctl: n = 4) and nonpregnant (Group I: n = 4; Group II: n = 4; Ctl: n = 3) animals on Days 6, 13 and 20 post-AI. Animals deemed pregnant on Day 28 were again biopsied on Day 42. Additionally, blood samples were taken from the vena sacralis mediana at the time of each biopsy. The biopsies were analysed regarding the relative abundance of 8 gene transcripts (VEGF, ECE1, PLA2G4A, PTGS2, PTGFR, PPARG, STAR and HSD3B1) via RT-qPCR. Blood samples were analysed for their concentration of progesterone through a radioimmunoassay (RIA). Statistical analysis for both datasets was performed via a 3-way ANOVA with adjoining Tukey test. The expression of 7 of these genes was affected by 1, 2, or all 3 of the following factors: day of cycle (VEGF, ECE1, PLA2G4A, PTGFR, STAR and HSD3B1), pregnancy status (ECE1, PTGFR and HSD3B1) and CLA supplementation (ECE1, PTGS2, PTGFR, STAR and HSD3B1). The effects of the CLA supplementation could be seen as a down-regulation in the mentioned gene transcripts. Progesterone concentrations differed significantly in dependency of the pregnancy status (significantly higher in pregnant vs nonpregnant individuals) of the animals, as well as during the days of the oestrous cycle (physiological progesterone curve with highest values on Day 13 of these samples). An effect of the oral supplementation with CLA could be detected during the early luteal phase (Day 6) where animals that had received 100 g of CLA day–1 had a significantly lower blood progesterone concentration than those receiving 50 g of CLA day–1 or no CLA. In conclusion, dietary CLA supplementation has an effect on luteal gene expression and functionality. The authors thank the DFG (German Research Foundation) for their financial support (PAK286/1; WR154/1-1).

Detection of group I and group II introns in a Mexican Bacillus thuringiensis collection

2010 ◽  
Author(s):  
A. Espino-Vázquez ◽  
A. Solís-Soto ◽  
H.A. Luna-Olvera ◽  
H. Medrano-Roldán ◽  
B. Pereyra-Alférez
Keyword(s):  
Bacillus Thuringiensis ◽  
Group Ii Introns ◽  
Group I ◽  
Group Ii

scholarly journals A Self-Splicing Group I Intron in DNA Polymerase Genes of T7-Like Bacteriophages

2004 ◽  
Vol 186 (23) ◽  
pp. 8153-8155 ◽  
Author(s):  
Richard P. Bonocora ◽  
David A. Shub
Keyword(s):  
Dna Polymerase ◽  
Group I Intron ◽  
Group I Introns ◽  
Homing Endonucleases ◽  
Structural Element ◽  
Group I ◽  
Close Relatives ◽  
Self Splicing

ABSTRACT Group I introns are inserted into genes of a wide variety of bacteriophages of gram-positive bacteria. However, among the phages of enteric and other gram-negative proteobacteria, introns have been encountered only in phage T4 and several of its close relatives. Here we report the insertion of a self-splicing group I intron in the coding sequence of the DNA polymerase genes of ΦI and W31, phages that are closely related to T7. The introns belong to subgroup IA2 and both contain an open reading frame, inserted into structural element P6a, encoding a protein belonging to the HNH family of homing endonucleases. The introns splice efficiently in vivo and self-splice in vitro under mild conditions of ionic strength and temperature. We conclude that there is no barrier for maintenance of group I introns in phages of proteobacteria.

scholarly journals Group II intron inhibits conjugative relaxase expression in bacteria by mRNA targeting

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Guosheng Qu ◽  
Carol Lyn Piazza ◽  
Dorie Smith ◽  
Marlene Belfort
Keyword(s):  
Gene Expression ◽  
Mrna Level ◽  
Mobile Element ◽  
Housekeeping Genes ◽  
Group Ii Intron ◽  
Conjugative Plasmid ◽  
Group Ii Introns ◽  
Potential Force ◽  
Spliceosomal Introns ◽  
Group Ii

Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis, inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA. The spliced intron targets the relaxase mRNA and reopens ligated exons, causing major mRNA loss. Taken together, this study provides an explanation for the distribution and paucity of group II introns in bacteria, and suggests a potential force for those introns to evolve into spliceosomal introns.

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