Limits...
The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat.

Tourasse NJ, Shtaida N, Khozin-Goldberg I, Boussiba S, Vallon O - BMC Genomics (2015)

Bottom Line: Incisa Mitochondrial Palindrome), found 19 times in the genome.The mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression.Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.

View Article: PubMed Central - PubMed

Affiliation: Institut de Biologie Physico-Chimique, UMR CNRS 7141 - Université Pierre et Marie Curie, Paris, France. nicolas.tourasse@ibpc.fr.

ABSTRACT

Background: Lobosphaera incisa, formerly known as Myrmecia incisa and then Parietochloris incisa, is an oleaginous unicellular green alga belonging to the class Trebouxiophyceae (Chlorophyta). It is the richest known plant source of arachidonic acid, an ω-6 poly-unsaturated fatty acid valued by the pharmaceutical and baby-food industries. It is therefore an organism of high biotechnological interest, and we recently reported the sequence of its chloroplast genome.

Results: We now report the complete sequence of the mitochondrial genome of L. incisa from high-throughput Illumina short-read sequencing. The circular chromosome of 69,997 bp is predicted to encode a total of 64 genes, some harboring specific self-splicing group I and group II introns. Overall, the gene content is highly similar to that of the mitochondrial genomes of other Trebouxiophyceae, with 34 protein-coding, 3 rRNA, and 27 tRNA genes. Genes are distributed in two clusters located on different DNA strands, a bipartite arrangement that suggests expression from two divergent promoters yielding polycistronic primary transcripts. The L. incisa mitochondrial genome contains families of intergenic dispersed DNA repeat sequences that are not shared with other known mitochondrial genomes of Trebouxiophyceae. The most peculiar feature of the genome is a repetitive palindromic repeat, the LIMP (L. Incisa Mitochondrial Palindrome), found 19 times in the genome. It is formed by repetitions of an AACCA pentanucleotide, followed by an invariant 7-nt loop and a complementary repeat of the TGGTT motif. Analysis of the genome sequencing reads indicates that the LIMP can be a substrate for large-scale genomic rearrangements. We speculate that LIMPs can act as origins of replication. Deep sequencing of the L. incisa transcriptome also suggests that the LIMPs with long stems are sites of transcript processing. The genome also contains five copies of a related palindromic repeat, the HyLIMP, with a 10-nt motif related to that of the LIMP.

Conclusions: The mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression. Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.

No MeSH data available.


Related in: MedlinePlus

Sequence and predicted secondary structure of LIMP repeats. a Alignment of all LIMP copies along with 80 bp of flanking sequence from both sides. LIMPs have been ordered so as to see the similarity between their flanks. For nine LIMPs, the reverse-complemented sequence is also shown to illustrate the fact that a few LIMPs have similar complementary flanks. b Predicted single-stranded RNA secondary structure of a LIMP, using LIMP #2 as an example. c Predicted double-stranded DNA secondary structure of the cruciform at LIMP #2
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Fig2: Sequence and predicted secondary structure of LIMP repeats. a Alignment of all LIMP copies along with 80 bp of flanking sequence from both sides. LIMPs have been ordered so as to see the similarity between their flanks. For nine LIMPs, the reverse-complemented sequence is also shown to illustrate the fact that a few LIMPs have similar complementary flanks. b Predicted single-stranded RNA secondary structure of a LIMP, using LIMP #2 as an example. c Predicted double-stranded DNA secondary structure of the cruciform at LIMP #2

Mentions: One of the repeats in the mitochondrial genome of L. incisa stands out as highly unusual, because it is both palindromic and internally repetitive. We termed it the LIMP (L. IncisaMitochondrial Palindrome). Nineteen copies are found in the genome (Table 2). Their structure can be summarized by the following pattern: 5’-(AACCA)m[AATGAAA or TTTCATT] (TGGTT)n-3’, where 2 ≤ (m,n) ≤13 (Table 2 and Fig. 2a). Each LIMP is by itself repetitive, as it comprises a pentanucleotide motif (AACCA) that is repeated a variable number of times, and palindromic as the complementary motif TGGTT is repeated downstream, after a short loop. Hereafter, AACCA and TGGTT pentanucleotides will be referred to as “A-units” and “T-units”, respectively. The number of A- and T-units for a given LIMP can differ. The two branches of the stem are separated by a conserved 7-nt loop that can be found in either of two orientations: AATGAAA or TTTCATT (reading on the plus strand). The first orientation will hereafter be referred to as +, the second one as -. LIMP copies are always intergenic, and found in both the clockwise and the counterclockwise gene clusters, with + and - orientations about equally represented (Table 2, Fig.2a). On the RNA, the LIMP sequence will always read 5’-AACCA…UGGUU-3’, while the loop will read either AAUGAAA or UUUCAUU. While the loop sequence is invariant, variants of the pentanucleotide can be found just next to some LIMPs (AGCCA and CGGTG flanking LIMP #2; GTCCA GACCA left of LIMPs #5, 8, 9 and 15, which leads to an increase in the length of the palindrome and in some cases makes the LIMP almost symmetrical; see Fig. 2a). As another evidence for mutational decay of the LIMP ends, 79 LIMP remnants were also found in the genome, containing a perfect or near-perfect 11–20 nt fragment of the LIMP (including the loop) but unable to form a stem-loop. These remnants often reside near bona fide LIMPs or are associated with other repeat sequences.Table 2


The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat.

Tourasse NJ, Shtaida N, Khozin-Goldberg I, Boussiba S, Vallon O - BMC Genomics (2015)

Sequence and predicted secondary structure of LIMP repeats. a Alignment of all LIMP copies along with 80 bp of flanking sequence from both sides. LIMPs have been ordered so as to see the similarity between their flanks. For nine LIMPs, the reverse-complemented sequence is also shown to illustrate the fact that a few LIMPs have similar complementary flanks. b Predicted single-stranded RNA secondary structure of a LIMP, using LIMP #2 as an example. c Predicted double-stranded DNA secondary structure of the cruciform at LIMP #2
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4524435&req=5

Fig2: Sequence and predicted secondary structure of LIMP repeats. a Alignment of all LIMP copies along with 80 bp of flanking sequence from both sides. LIMPs have been ordered so as to see the similarity between their flanks. For nine LIMPs, the reverse-complemented sequence is also shown to illustrate the fact that a few LIMPs have similar complementary flanks. b Predicted single-stranded RNA secondary structure of a LIMP, using LIMP #2 as an example. c Predicted double-stranded DNA secondary structure of the cruciform at LIMP #2
Mentions: One of the repeats in the mitochondrial genome of L. incisa stands out as highly unusual, because it is both palindromic and internally repetitive. We termed it the LIMP (L. IncisaMitochondrial Palindrome). Nineteen copies are found in the genome (Table 2). Their structure can be summarized by the following pattern: 5’-(AACCA)m[AATGAAA or TTTCATT] (TGGTT)n-3’, where 2 ≤ (m,n) ≤13 (Table 2 and Fig. 2a). Each LIMP is by itself repetitive, as it comprises a pentanucleotide motif (AACCA) that is repeated a variable number of times, and palindromic as the complementary motif TGGTT is repeated downstream, after a short loop. Hereafter, AACCA and TGGTT pentanucleotides will be referred to as “A-units” and “T-units”, respectively. The number of A- and T-units for a given LIMP can differ. The two branches of the stem are separated by a conserved 7-nt loop that can be found in either of two orientations: AATGAAA or TTTCATT (reading on the plus strand). The first orientation will hereafter be referred to as +, the second one as -. LIMP copies are always intergenic, and found in both the clockwise and the counterclockwise gene clusters, with + and - orientations about equally represented (Table 2, Fig.2a). On the RNA, the LIMP sequence will always read 5’-AACCA…UGGUU-3’, while the loop will read either AAUGAAA or UUUCAUU. While the loop sequence is invariant, variants of the pentanucleotide can be found just next to some LIMPs (AGCCA and CGGTG flanking LIMP #2; GTCCA GACCA left of LIMPs #5, 8, 9 and 15, which leads to an increase in the length of the palindrome and in some cases makes the LIMP almost symmetrical; see Fig. 2a). As another evidence for mutational decay of the LIMP ends, 79 LIMP remnants were also found in the genome, containing a perfect or near-perfect 11–20 nt fragment of the LIMP (including the loop) but unable to form a stem-loop. These remnants often reside near bona fide LIMPs or are associated with other repeat sequences.Table 2

Bottom Line: Incisa Mitochondrial Palindrome), found 19 times in the genome.The mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression.Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.

View Article: PubMed Central - PubMed

Affiliation: Institut de Biologie Physico-Chimique, UMR CNRS 7141 - Université Pierre et Marie Curie, Paris, France. nicolas.tourasse@ibpc.fr.

ABSTRACT

Background: Lobosphaera incisa, formerly known as Myrmecia incisa and then Parietochloris incisa, is an oleaginous unicellular green alga belonging to the class Trebouxiophyceae (Chlorophyta). It is the richest known plant source of arachidonic acid, an ω-6 poly-unsaturated fatty acid valued by the pharmaceutical and baby-food industries. It is therefore an organism of high biotechnological interest, and we recently reported the sequence of its chloroplast genome.

Results: We now report the complete sequence of the mitochondrial genome of L. incisa from high-throughput Illumina short-read sequencing. The circular chromosome of 69,997 bp is predicted to encode a total of 64 genes, some harboring specific self-splicing group I and group II introns. Overall, the gene content is highly similar to that of the mitochondrial genomes of other Trebouxiophyceae, with 34 protein-coding, 3 rRNA, and 27 tRNA genes. Genes are distributed in two clusters located on different DNA strands, a bipartite arrangement that suggests expression from two divergent promoters yielding polycistronic primary transcripts. The L. incisa mitochondrial genome contains families of intergenic dispersed DNA repeat sequences that are not shared with other known mitochondrial genomes of Trebouxiophyceae. The most peculiar feature of the genome is a repetitive palindromic repeat, the LIMP (L. Incisa Mitochondrial Palindrome), found 19 times in the genome. It is formed by repetitions of an AACCA pentanucleotide, followed by an invariant 7-nt loop and a complementary repeat of the TGGTT motif. Analysis of the genome sequencing reads indicates that the LIMP can be a substrate for large-scale genomic rearrangements. We speculate that LIMPs can act as origins of replication. Deep sequencing of the L. incisa transcriptome also suggests that the LIMPs with long stems are sites of transcript processing. The genome also contains five copies of a related palindromic repeat, the HyLIMP, with a 10-nt motif related to that of the LIMP.

Conclusions: The mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression. Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.

No MeSH data available.


Related in: MedlinePlus