Expression Profiling of Organellar Genes

Cardi, Teodoro; Giegé, Philippe; Kahlau, Sabine; Scotti, Nunzia

doi:10.1007/978-94-007-2920-9_14

Cited by 8 publications

(6 citation statements)

References 253 publications

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“…( 62 )). It appears that incompletely edited transcripts in plant mitochondria are either not translated or, if translated, the resulting proteins are instable and readily degraded (( 63 ); reviewed in ( 64 )).…”

Section: Resultsmentioning

confidence: 99%

Novel modes of RNA editing in mitochondria

et al. 2016

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Gene structure and expression in diplonemid mitochondria are unparalleled. Genes are fragmented in pieces (modules) that are separately transcribed, followed by the joining of module transcripts to contiguous RNAs. Some instances of unique uridine insertion RNA editing at module boundaries were noted, but the extent and potential occurrence of other editing types remained unknown. Comparative analysis of deep transcriptome and genome data from Diplonema papillatum mitochondria reveals ∼220 post-transcriptional insertions of uridines, but no insertions of other nucleotides nor deletions. In addition, we detect in total 114 substitutions of cytosine by uridine and adenosine by inosine, amassed into unusually compact clusters. Inosines in transcripts were confirmed experimentally. This is the first report of adenosine-to-inosine editing of mRNAs and ribosomal RNAs in mitochondria. In mRNAs, editing causes mostly amino-acid additions and non-synonymous substitutions; in ribosomal RNAs, it permits formation of canonical secondary structures. Two extensively edited transcripts were compared across four diplonemids. The pattern of uridine-insertion editing is strictly conserved, whereas substitution editing has diverged dramatically, but still rendering diplonemid proteins more similar to other eukaryotic orthologs. We posit that RNA editing not only compensates but also sustains, or even accelerates, ultra-rapid evolution of genome structure and sequence in diplonemid mitochondria.

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Section: Resultsmentioning

confidence: 99%

Novel modes of RNA editing in mitochondria

et al. 2016

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“…One consequence of less efficient purifying selection is the accumulation of slightly deleterious amino-acid changes (Moran, 1996). In turn, cis and/or trans-acting small RNAs we identified here may be important inhibitors of these potentially toxic proteins (Kuo and Ochman, 2010 (Mercer et al, 2011;Cardi et al, 2012). Small RNAs in free-living bacteria have a role in one type of post-transcriptional gene regulation (Waters and Storz, 2009;Gottesman and Storz, 2011;Storz et al, 2011).…”

Section: Extensive Asrna Expression In Buchneramentioning

confidence: 91%

Widespread expression of conserved small RNAs in small symbiont genomes

2014

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Genome architecture of a microbe markedly changes when it transitions from a free-living lifestyle to an obligate symbiotic association within eukaryotic cells. These symbiont genomes experience numerous rearrangements and massive gene loss, which is expected to radically alter gene regulatory networks compared with those of free-living relatives. As such, it remains unclear whether and how these small symbiont genomes regulate gene expression. Here, using a label-free mass-spec quantification approach we found that differential protein regulation occurs in Buchnera, a model symbiont with a reduced genome, when it transitions between two distinct life stages. However, differential mRNA expression could not be detected between Buchnera life stages, despite the presence of a small number of putative transcriptional regulators. Instead a comparative analysis of small RNA expression profiles among five divergent Buchnera lineages, spanning a variety of Buchnera life stages, reveals 140 novel intergenic and antisense small RNAs and 517 untranslated regions that were significantly expressed, some of which have been conserved for B65 million years. In addition, the majority of these small RNAs exhibit both sequence covariation and thermodynamic stability, indicators of a potential structural RNA role. Together, these data suggest that gene regulation at the post-transcriptional level may be important in Buchnera. This is the first study to empirically identify Buchnera small RNAs, and we propose that these novel small RNAs may facilitate post-transcriptional regulation through translational inhibition/activation, and/ or transcript stability. Ultimately, post-transcriptional regulation may shape metabolic complementation between Buchnera and its aphid host, thus impacting the animal's ecology and evolution.

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“…While many of these proteins have lost the canonical means of transcriptional regulation and did not reveal differential expression at the mRNA level, most of these genes have either conserved antisense RNAs (asRNAs) expressed within their transcriptional unit, or conserved small RNAs (sRNAs) expressed adjacent to the coding sequences (Hansen & Degnan, ). Consequently, posttranscriptional gene regulation observed in Buchnera (Hansen & Degnan, ) may utilize these conserved sRNAs to inhibit/activate translation, as seen in organelles (Mercer et al ., ; Cardi et al ., ) and obligate pathogens, such as Mycoplasma , Rickettsia , and Wolbachia (Güell et al ., ; Mayoral et al ., ).…”

Section: Aphidsmentioning

confidence: 99%

The evolutionary development of plant‐feeding insects and their nutritional endosymbionts

Skidmore

Hansen

2017

Insect Science

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Herbivorous insects have evolved diverse mechanisms enabling them to feed on plants with suboptimal nutrient availability. Low nutrient availability negatively impacts insect herbivore development and fitness. To overcome this obstacle numerous insect lineages have evolved intimate associations with nutritional endosymbionts. This is especially true for insects that specialize on nitrogen-poor substrates, as these insects are highly dependent on intracellular symbionts to provide nitrogen lacking in their insect host's diet. Emerging evidence in these systems suggest that the symbiont's and/or the insect's biosynthetic pathways are dynamically regulated throughout the insect's development to potentially cope with the insect's changing nutritional demands. In this review, we evaluate the evolutionary development of symbiotic insect cells (bacteriocytes) by comparing and contrasting genes and mechanisms involved in maintaining and regulating the nutritional symbiosis throughout insect development in a diversity of insect herbivore-endosymbiont associations. With new advances in genome sequencing and functional genomics, we evaluate to what extent nutritional symbioses are shaped by (i) the regulation of symbiont titer, (ii) the regulation of insect symbiosis genes, and (iii) the regulation of symbiont genes. We discuss how important these mechanisms are for the biosynthesis of essential amino acids and vitamins across insect life stages in divergent insect-symbiont systems. We conclude by suggesting future directions of research to further elucidate the evolutionary development of bacteriocytes and the impact of these nutritional symbioses on insect-plant interactions.

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Expression Profiling of Organellar Genes

Cited by 8 publications

References 253 publications

Novel modes of RNA editing in mitochondria

Novel modes of RNA editing in mitochondria

Widespread expression of conserved small RNAs in small symbiont genomes

The evolutionary development of plant‐feeding insects and their nutritional endosymbionts

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