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A chloroplast is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in the cells. The ATP and NADPH is then used to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat.
Symbiogenesis is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales bacteria, while chloroplasts are thought to be related to cyanobacteria.
The phragmoplast is a plant cell specific structure that forms during late cytokinesis. It serves as a scaffold for cell plate assembly and subsequent formation of a new cell wall separating the two daughter cells. The phragmoplast can only be observed in Phragmoplastophyta, a clade that includes the Coleochaetophyceae, Zygnematophyceae, Mesotaeniaceae, and Embryophyta. Some algae use another type of microtubule array, a phycoplast, during cytokinesis.
RNA editing is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase. It occurs in all living organisms and is one of the most evolutionarily conserved properties of RNAs. RNA editing may include the insertion, deletion, and base substitution of nucleotides within the RNA molecule. RNA editing is relatively rare, with common forms of RNA processing not usually considered as editing. It can affect the activity, localization as well as stability of RNAs, and has been linked with human diseases.
A nuclear gene is a gene that has its DNA nucleotide sequence physically situated within the cell nucleus of a eukaryotic organism. This term is employed to differentiate nuclear genes, which are located in the cell nucleus, from genes that are found in mitochondria or chloroplasts. The vast majority of genes in eukaryotes are nuclear.
Extrachromosomal DNA is any DNA that is found off the chromosomes, either inside or outside the nucleus of a cell. Most DNA in an individual genome is found in chromosomes contained in the nucleus. Multiple forms of extrachromosomal DNA exist, and, while some of these serve important biological functions, they can also play a role in diseases such as cancer.
In order for a virus to infect a plant, it must be able to move between cells so it can spread throughout the plant. Plant cell walls make this moving/spreading quite difficult and therefore, for this to occur, movement proteins must be present. A movement protein (MP) is a specific virus-encoded protein that is thought to be a general feature of plant genomes. They allow for local and systemic viral spread throughout a plant. MPs were first studied in the Tobacco Mosaic Virus (TMV) where it was found that viruses were unable to spread without the presence of a specific protein. In general, the plant viruses first, move within the cell from replication sites to the plasmodesmata (PD). Then, the virus is able to go through the PD and spread to other cells. This process is controlled through MPs. Different MPs use different mechanisms and pathways to regulate this spread of some viruses. Nearly all plants express at least one MP, while some can encode many different MPs which help with cell to cell viral transmission. They serve to increase the size exclusion limits (SEL) of plasmodesmata to allow for greater spread of the virus.
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are complexes of RNA and protein present in the cell nucleus during gene transcription and subsequent post-transcriptional modification of the newly synthesized RNA (pre-mRNA). The presence of the proteins bound to a pre-mRNA molecule serves as a signal that the pre-mRNA is not yet fully processed and therefore not ready for export to the cytoplasm. Since most mature RNA is exported from the nucleus relatively quickly, most RNA-binding protein in the nucleus exist as heterogeneous ribonucleoprotein particles. After splicing has occurred, the proteins remain bound to spliced introns and target them for degradation.
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
The MADS box is a conserved sequence motif. The genes which contain this motif are called the MADS-box gene family. The MADS box encodes the DNA-binding MADS domain. The MADS domain binds to DNA sequences of high similarity to the motif CC[A/T]6GG termed the CArG-box. MADS-domain proteins are generally transcription factors. The length of the MADS-box reported by various researchers varies somewhat, but typical lengths are in the range of 168 to 180 base pairs, i.e. the encoded MADS domain has a length of 56 to 60 amino acids. There is evidence that the MADS domain evolved from a sequence stretch of a type II topoisomerase in a common ancestor of all extant eukaryotes.
Polynucleotide Phosphorylase (PNPase) is a bifunctional enzyme with a phosphorolytic 3' to 5' exoribonuclease activity and a 3'-terminal oligonucleotide polymerase activity. That is, it dismantles the RNA chain starting at the 3' end and working toward the 5' end. It also synthesizes long, highly heteropolymeric tails in vivo. It accounts for all of the observed residual polyadenylation in strains of Escherichia coli missing the normal polyadenylation enzyme. Discovered by Marianne Grunberg-Manago working in Severo Ochoa's lab in 1955, the RNA-polymerization activity of PNPase was initially believed to be responsible for DNA-dependent synthesis of messenger RNA, a notion that was disproven by the late 1950s.
The pentatricopeptide repeat (PPR) is a 35-amino acid sequence motif. Pentatricopeptide-repeat-containing proteins are a family of proteins commonly found in the plant kingdom. They are distinguished by the presence of tandem degenerate PPR motifs and by the relative lack of introns in the genes coding for them.
Polypyrimidine tract-binding protein 1 is a protein that in humans is encoded by the PTBP1 gene.
Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, a great number of chloroplast DNAs from various species have been sequenced.
The bZIP intron RNA motif is an RNA structure guiding splicing of a non-canonical intron from bZIP-containing genes called HAC1 in yeast, XBP1 in Metazoa, Hxl1 or Cib1 in Basidiomycota and bZIP60 in plants. Splicing is performed independently of the spliceosome by Ire1, a kinase with endoribonuclease activity. Exons are joined by a tRNA ligase. Recognition of the intron splice sites is mediated by a base-paired secondary structure of the mRNA that forms at the exon/intron boundaries. Splicing of the bZIP intron is a key regulatory step in the unfolded protein response (UPR). The Ire-mediated unconventional splicing was first described for HAC1 in S. cerevisiae.
In molecular biology, the CRM domain is an approximately 100-amino acid RNA-binding domain. The name CRM has been suggested to reflect the functions established for four characterised members of the family: Zea mays (Maize) CRS1, CAF1 and CAF2 proteins and the Escherichia coli protein YhbY. Proteins containing the CRM domain are found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets.
Maureen Hanson is an American molecular biologist and Liberty Hyde Bailey Professor in the Department of Molecular Biology and Genetics at Cornell University in Ithaca, New York. She is a joint member of the Section of Plant Biology and Director of the Center for Enervating Neuroimmune Disease. Her research concerns gene expression in chloroplasts and mitochondria, photosynthesis, and the molecular basis of the disease Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).
Wojciech Maciej Karlowski is a Polish biologist specializing in molecular biology and bioinformatics, and a full professor in biological sciences. He is Head of the Department of Computational Biology at the Faculty of Biology at the Adam Mickiewicz University in Poznan. His major scientific interests include identification of non-coding RNAs, genomics, high-throughput analyses, and functional annotation of biological sequences.
Pal Maliga is a plant molecular biologist. He is Distinguished Professor of Plant Biology and Laboratory Director at the Waksman Institute of Microbiology, Rutgers University. He is known for developing the technology of chloroplast genome engineering in land plants and its applications in basic science and biotechnology.
Christoph Benning is a German–American plant biologist. He is an MSU Foundation Professor and University Distinguished Professor at Michigan State University. Benning's research into lipid metabolism in plants, algae and photosynthetic bacteria, led him to be named Editor-in-Chief of The Plant Journal in October 2008.
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- 1 2 Barkan, Alice; Small, Ian (2014-04-29). "Pentatricopeptide Repeat Proteins in Plants". Annual Review of Plant Biology. 65 (1): 415–442. doi: 10.1146/annurev-arplant-050213-040159 . ISSN 1543-5008. PMID 24471833.
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- ↑ Ostheimer, G. J. (2003-08-01). "Group II intron splicing factors derived by diversification of an ancient RNA-binding domain". The EMBO Journal. 22 (15): 3919–3929. doi:10.1093/emboj/cdg372. ISSN 1460-2075. PMC 169045 . PMID 12881426.
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- ↑ McDermott, James J.; Watkins, Kenneth P.; Williams-Carrier, Rosalind; Barkan, Alice (2019-08-01). "Ribonucleoprotein Capture by in Vivo Expression of a Designer Pentatricopeptide Repeat Protein in Arabidopsis". The Plant Cell. 31 (8): 1723–1733. doi:10.1105/tpc.19.00177. ISSN 1040-4651. PMC 6713294 . PMID 31123048.
- ↑ Rojas, Margarita; Yu, Qiguo; Williams-Carrier, Rosalind; Maliga, Pal; Barkan, Alice (2019). "Engineered PPR proteins as inducible switches to activate the expression of chloroplast transgenes". Nature Plants. 5 (5): 505–511. doi:10.1038/s41477-019-0412-1. ISSN 2055-0278. PMID 31036912. S2CID 139103684.
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