Maturase K

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Maturase K
Identifiers
Organism Arabidopsis thaliana, plants
SymbolmatK
Alt. symbolsycf14
Entrez 844797
RefSeq (mRNA) NP_051040.2
UniProt P56784
Search for
Structures Swiss-model
Domains InterPro
MatK/TrnK, N-terminal (inactive RT)
Identifiers
SymbolMatK_N
Pfam PF01824
InterPro IPR024942
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
Location of the matK gene in the chloroplast genome of Arabidopsis thaliana. matK is one of the protein-coding genes involved in functions other than photosynthetic reactions (red boxes). matK maps at the 2-3.5 kb coordinates. Plastomap of Arabidopsis thaliana.svg
Location of the matK gene in the chloroplast genome of Arabidopsis thaliana . matK is one of the protein-coding genes involved in functions other than photosynthetic reactions (red boxes). matK maps at the 2–3.5 kb coordinates.

Maturase K (matK) is a plant plastidial gene. [1] The protein it encodes is an organelle intron maturase, a protein that splices Group II introns. It is essential for in vivo splicing of Group II introns. [2] Amongst other maturases, this protein retains only a well conserved domain X and remnants of a reverse transcriptase domain. [3]

Universal matK primers can be used for DNA barcoding of angiosperms. [4]

See also

Related Research Articles

An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word intron is derived from the term intragenic region, i.e., a region inside a gene. The term intron refers to both the DNA sequence within a gene and the corresponding RNA sequence in RNA transcripts. The non-intron sequences that become joined by this RNA processing to form the mature RNA are called exons.

<span class="mw-page-title-main">Retroposon</span>

Retroposons are repetitive DNA fragments which are inserted into chromosomes after they had been reverse transcribed from any RNA molecule.

<span class="mw-page-title-main">Reverse transcriptase</span> Enzyme which generates DNA

A reverse transcriptase (RT) is an enzyme used to convert RNA genome to DNA, a process termed reverse transcription. Reverse transcriptases are used by viruses such as HIV and hepatitis B to replicate their genomes, by retrotransposon mobile genetic elements to proliferate within the host genome, and by eukaryotic cells to extend the telomeres at the ends of their linear chromosomes. Contrary to a widely held belief, the process does not violate the flows of genetic information as described by the classical central dogma, as transfers of information from RNA to DNA are explicitly held possible.

<span class="mw-page-title-main">Ribonuclease H</span> Enzyme family

Ribonuclease H is a family of non-sequence-specific endonuclease enzymes that catalyze the cleavage of RNA in an RNA/DNA substrate via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from bacteria to archaea to eukaryotes.

<span class="mw-page-title-main">Retrotransposon</span> Type of genetic component

Retrotransposons are mobile elements which move in the host genome by converting their transcribed RNA into DNA through the reverse transcription. Thus, they differ from Class II transposable elements, or DNA transposons, in utilizing an RNA intermediate for the transposition and leaving the transposition donor site unchanged.

Exon shuffling is a molecular mechanism for the formation of new genes. It is a process through which two or more exons from different genes can be brought together ectopically, or the same exon can be duplicated, to create a new exon-intron structure. There are different mechanisms through which exon shuffling occurs: transposon mediated exon shuffling, crossover during sexual recombination of parental genomes and illegitimate recombination.

<span class="mw-page-title-main">Multicopy single-stranded DNA</span>

Multicopy single-stranded DNA (msDNA) is a type of extrachromosomal satellite DNA that consists of a single-stranded DNA molecule covalently linked via a 2'-5'phosphodiester bond to an internal guanosine of an RNA molecule. The resultant DNA/RNA chimera possesses two stem-loops joined by a branch similar to the branches found in RNA splicing intermediates. The coding region for msDNA, called a "retron", also encodes a type of reverse transcriptase, which is essential for msDNA synthesis.

<span class="mw-page-title-main">Long terminal repeat</span> DNA sequence

A long terminal repeat (LTR) is a pair of identical sequences of DNA, several hundred base pairs long, which occur in eukaryotic genomes on either end of a series of genes or pseudogenes that form a retrotransposon or an endogenous retrovirus or a retroviral provirus. All retroviral genomes are flanked by LTRs, while there are some retrotransposons without LTRs. Typically, an element flanked by a pair of LTRs will encode a reverse transcriptase and an integrase, allowing the element to be copied and inserted at a different location of the genome. Copies of such an LTR-flanked element can often be found hundreds or thousands of times in a genome. LTR retrotransposons comprise about 8% of the human genome.

<span class="mw-page-title-main">Group II intron</span> Class of self-catalyzing ribozymes

Group II introns are a large class of self-catalytic ribozymes and mobile genetic elements found within the genes of all three domains of life. Ribozyme activity can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing. In contrast to group I introns, intron excision occurs in the absence of GTP and involves the formation of a lariat, with an A-residue branchpoint strongly resembling that found in lariats formed during splicing of nuclear pre-mRNA. It is hypothesized that pre-mRNA splicing may have evolved from group II introns, due to the similar catalytic mechanism as well as the structural similarity of the Group II Domain V substructure to the U6/U2 extended snRNA. Finally, their ability to site-specifically insert into DNA sites has been exploited as a tool for biotechnology. For example, group II introns can be modified to make site-specific genome insertions and deliver cargo DNA such as reporter genes or lox sites

<span class="mw-page-title-main">Group I catalytic intron</span> Large self-splicing ribozymes

Group I introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of nine paired regions (P1-P9). These fold to essentially two domains – the P4-P6 domain and the P3-P9 domain. The secondary structure mark-up for this family represents only this conserved core. Group I introns often have long open reading frames inserted in loop regions.

<span class="mw-page-title-main">Retron</span>

A retron is a distinct DNA sequence found in the genome of many bacteria species that codes for reverse transcriptase and a unique single-stranded DNA/RNA hybrid called multicopy single-stranded DNA (msDNA). Retron msr RNA is the non-coding RNA produced by retron elements and is the immediate precursor to the synthesis of msDNA. The retron msr RNA folds into a characteristic secondary structure that contains a conserved guanosine residue at the end of a stem loop. Synthesis of DNA by the retron-encoded reverse transcriptase (RT) results in a DNA/RNA chimera which is composed of small single-stranded DNA linked to small single-stranded RNA. The RNA strand is joined to the 5′ end of the DNA chain via a 2′–5′ phosphodiester linkage that occurs from the 2′ position of the conserved internal guanosine residue.

LtrA is an open reading frame found in the Lactococcus lactis group II introns LtrB. It is an intron-encoded protein, which consists of three subdomains: a reverse-transcriptase/maturase, DNA endonuclease, and DNA/RNA binding domain. LtrA helps to capture and stabilize the catalytically active conformation of the LtrB group II intron RNA. It also functions in group II intron retrohoming.

<span class="mw-page-title-main">LTR retrotransposon</span> Class I transposable element

LTR retrotransposons are class I transposable elements (TEs) characterized by the presence of long terminal repeats (LTRs) directly flanking an internal coding region. As retrotransposons, they mobilize through reverse transcription of their mRNA and integration of the newly created cDNA into another genomic location. Their mechanism of retrotransposition is shared with retroviruses, with the difference that the rate of horizontal transfer in LTR-retrotransposons is much lower than the vertical transfer by passing active TE insertions to the progeny. LTR retrotransposons that form virus-like particles are classified under Ortervirales.

Numerous key discoveries in biology have emerged from studies of RNA, including seminal work in the fields of biochemistry, genetics, microbiology, molecular biology, molecular evolution, and structural biology. As of 2010, 30 scientists have been awarded Nobel Prizes for experimental work that includes studies of RNA. Specific discoveries of high biological significance are discussed in this article.

A conserved non-coding sequence (CNS) is a DNA sequence of noncoding DNA that is evolutionarily conserved. These sequences are of interest for their potential to regulate gene production.

<span class="mw-page-title-main">Long interspersed nuclear element</span>

Long interspersed nuclear elements (LINEs) are a group of non-LTR retrotransposons that are widespread in the genome of many eukaryotes. LINEs contain an internal Pol II promoter to initiate transcription into mRNA, and encode one or two proteins, ORF1 and ORF2. The functional domains present within ORF1 vary greatly among LINEs, but often exhibit RNA/DNA binding activity. ORF2 is essential to successful retrotransposition, and encodes a protein with both reverse transcriptase and endonuclease activity.

<span class="mw-page-title-main">Prp8</span>

Prp8 refers to both the Prp8 protein and Prp8 gene. Prp8's name originates from its involvement in pre-mRNA processing. The Prp8 protein is a large, highly conserved, and unique protein that resides in the catalytic core of the spliceosome and has been found to have a central role in molecular rearrangements that occur there. Prp8 protein is a major central component of the catalytic core in the spliceosome, and the spliceosome is responsible for splicing of precursor mRNA that contains introns and exons. Unexpressed introns are removed by the spliceosome complex in order to create a more concise mRNA transcript. Splicing is just one of many different post-transcriptional modifications that mRNA must undergo before translation. Prp8 has also been hypothesized to be a cofactor in RNA catalysis.

<span class="mw-page-title-main">Alan Lambowitz</span> American academic

Alan Lambowitz is a professor for the University of Texas at Austin in Molecular Biosciences and Oncology and has been instrumental in many bio-molecular processes and concepts, such as intron splicing and mitochondrial ribosomal assembly.

Ravindra N. Singh is an Indian American scientist, inventor and academic. He is a professor in the Department of Biomedical Sciences of the College of Veterinary Medicine at Iowa State University.

References

  1. Zoschke R, Nakamura M, Liere K, Sugiura M, Börner T, Schmitz-Linneweber C (February 2010). "An organellar maturase associates with multiple group II introns". Proceedings of the National Academy of Sciences of the United States of America. 107 (7): 3245–50. Bibcode:2010PNAS..107.3245Z. doi: 10.1073/pnas.0909400107 . PMC   2840290 . PMID   20133623.
  2. Ahlert D, Piepenburg K, Kudla J, Bock R (July 2006). "Evolutionary origin of a plant mitochondrial group II intron from a reverse transcriptase/maturase-encoding ancestor". Journal of Plant Research. 119 (4): 363–71. Bibcode:2006JPlR..119..363A. doi:10.1007/s10265-006-0284-0. PMID   16763758. S2CID   8277547.
  3. Mohr G, Perlman PS, Lambowitz AM (November 1993). "Evolutionary relationships among group II intron-encoded proteins and identification of a conserved domain that may be related to maturase function". Nucleic Acids Research. 21 (22): 4991–7. doi:10.1093/nar/21.22.4991. PMC   310608 . PMID   8255751.
  4. Jing YU, Jian-Hua XU, Shi-Liang ZH (May 2011). "New universal matK primers for DNA barcoding angiosperms". Journal of Systematics and Evolution. 49 (3): 176–81. doi: 10.1111/j.1759-6831.2011.00134.x . S2CID   86349548.