| Physcomitrella patens | |
|---|---|
 | |
Scientific classification  | |
| Kingdom: | Plantae |
| Division: | Bryophyta |
| Class: | Bryopsida |
| Subclass: | Funariidae |
| Order: | Funariales |
| Family: | Funariaceae |
| Genus: | Physcomitrella |
| Species: | P. patens |
| Binomial name | |
| Physcomitrella patens | |
| Synonyms [1] | |
Physcomitrella patens is a synonym of Physcomitrium patens, [2] [3] the spreading earthmoss. [4] It is a moss, a bryophyte used as a model organism for studies on plant evolution, development, and physiology. [3]
Physcomitrella patens is an early colonist of exposed mud and earth around the edges of pools of water. [5] [6] P. patens has a disjunct distribution in temperate parts of the world, with the exception of South America. [7] The standard laboratory strain is the "Gransden" isolate, collected by H. Whitehouse from Gransden Wood, in Cambridgeshire in 1962. [5]
Mosses share fundamental genetic and physiological processes with vascular plants, although the two lineages diverged early in land-plant evolution. [8] A comparative study between modern representatives of the two lines may give insight into the evolution of mechanisms that contribute to the complexity of modern plants. [8] In this context, P. patens is used as a model organism. [8] [3]
P. patens is one of a few known multicellular organisms with highly efficient homologous recombination. [9] [10] meaning that an exogenous DNA sequence can be targeted to a specific genomic position (a technique called gene targeting) to create knockout mosses. This approach is called reverse genetics and it is a powerful and sensitive tool to study the function of genes and, when combined with studies in higher plants such as Arabidopsis thaliana , can be used to study molecular plant evolution.[ citation needed ]
The targeted deletion or alteration of moss genes relies on the integration of a short DNA strand at a defined position in the genome of the host cell. Both ends of this DNA strand are engineered to be identical to this specific gene locus. The DNA construct is then incubated with moss protoplasts in the presence of polyethylene glycol. As mosses are haploid organisms, the regenerating moss filaments (protonemata) can be directly assayed for gene targeting within 6 weeks using PCR methods. [11] The first study using knockout moss appeared in 1998 and functionally identified ftsZ as a pivotal gene for the division of an organelle in a eukaryote. [12]
In addition, P. patens is increasingly used in biotechnology. Examples are the identification of moss genes with implications for crop improvement or human health [13] and the safe production of complex biopharmaceuticals in moss bioreactors. [14] By multiple gene knockout Physcomitrella plants were engineered that lack plant-specific post-translational protein glycosylation. These knockout mosses are used to produce complex biopharmaceuticals in a process called molecular farming. [15]
The genome of P. patens, with about 500 megabase pairs organized into 27 chromosomes, was completely sequenced in 2008. [8] [16]
Physcomitrella ecotypes, mutants, and transgenics are stored and made freely available to the scientific community by the International Moss Stock Center (IMSC). The accession numbers given by the IMSC can be used for publications to ensure safe deposit of newly described moss materials.[ citation needed ]
Like all mosses, the lifecycle of P. patens is characterized by an alternation of two generations: a haploid gametophyte that produces gametes and a diploid sporophyte where haploid spores are produced. [17]
A spore develops into a filamentous structure called protonema, composed of two types of cells – chloronema with large and numerous chloroplasts and caulonema with very fast growth. Protonema filaments grow exclusively by tip growth of their apical cells and can originate side branches from subapical cells. Some side-branch initial cells can differentiate into buds rather than side branches. These buds give rise to gametophores (0.5–5.0 mm [18] ), more complex structures bearing leaf-like structures, rhizoids, and the sexual organs: female archegonia and male antheridia. P. patens is monoicous, meaning that male and female organs are produced in the same plant. If water is available, flagellate sperm cells can swim from the antheridia to an archegonium and fertilize the egg within. The resulting diploid zygote develops into a sporophyte composed of a foot, seta, and capsule, where thousands of haploid spores are produced by meiosis. [19]
P. patens is an excellent model in which to analyze repair of DNA damages in plants by the homologous recombination pathway. Failure to repair double-strand breaks and other DNA damages in somatic cells by homologous recombination can lead to cell dysfunction or death, and when failure occurs during meiosis, it can cause loss of gametes. The genome sequence of P. patens has revealed the presence of numerous genes that encode proteins necessary for repair of DNA damages by homologous recombination and by other pathways. [8] PpRAD51, a protein at the core of the homologous recombination repair reaction, is required to preserve genome integrity in P. patens. [20] Loss of PpRAD51 causes marked hypersensitivity to the double-strand break-inducing agent bleomycin, indicating that homologous recombination is used for repair of somatic cell DNA damages. [20] PpRAD51 is also essential for resistance to ionizing radiation. [21]
The DNA mismatch repair protein PpMSH2 is a central component of the P. patens mismatch repair pathway that targets base pair mismatches arising during homologous recombination. The PpMsh2 gene is necessary in P. patens to preserve genome integrity. [22] Genes Ppmre11 and Pprad50 of P. patens encode components of the MRN complex, the principal sensor of DNA double-strand breaks. [23] These genes are necessary for accurate homologous recombinational repair of DNA damages in P. patens. Mutant plants defective in either Ppmre11 or Pprad50 exhibit severely restricted growth and development (possibly reflecting accelerated senescence), and enhanced sensitivity to UV-B and bleomycin-induced DNA damage compared to wild-type plants. [23]
P. patens was first described by Johann Hedwig in his 1801 work Species Muscorum Frondosorum, under the name Phascum patens. [1] Physcomitrella is sometimes treated as a synonym of the genus Aphanorrhegma , in which case P. patens is known as Aphanorrhegma patens. [26] The generic name Physcomitrella implies a resemblance to Physcomitrium , which is named for its large calyptra, unlike that of Physcomitrella. [18] In 2019 it was proposed that the correct name for this moss is Physcomitrium patens. [2] [3]
Meiosis is a special type of cell division of germ cells and apicomplexans in sexually-reproducing organisms that produces the gametes, the sperm or egg cells. It involves two rounds of division that ultimately result in four cells, each with only one copy of each chromosome (haploid). Additionally, prior to the division, genetic material from the paternal and maternal copies of each chromosome is crossed over, creating new combinations of code on each chromosome. Later on, during fertilisation, the haploid cells produced by meiosis from a male and a female will fuse to create a zygote, a cell with two copies of each chromosome again.
Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.
Gene knockouts are a widely used genetic engineering technique that involves the targeted removal or inactivation of a specific gene within an organism's genome. This can be done through a variety of methods, including homologous recombination, CRISPR-Cas9, and TALENs.
Mosses are small, non-vascular flowerless plants in the taxonomic division Bryophytasensu stricto. Bryophyta may also refer to the parent group bryophytes, which comprise liverworts, mosses, and hornworts. Mosses typically form dense green clumps or mats, often in damp or shady locations. The individual plants are usually composed of simple leaves that are generally only one cell thick, attached to a stem that may be branched or unbranched and has only a limited role in conducting water and nutrients. Although some species have conducting tissues, these are generally poorly developed and structurally different from similar tissue found in vascular plants. Mosses do not have seeds and after fertilisation develop sporophytes with unbranched stalks topped with single capsules containing spores. They are typically 0.2–10 cm (0.1–3.9 in) tall, though some species are much larger. Dawsonia, the tallest moss in the world, can grow to 50 cm (20 in) in height. There are approximately 12,000 species.
An archegonium, from the ancient Greek ἀρχή ("beginning") and γόνος ("offspring"), is a multicellular structure or organ of the gametophyte phase of certain plants, producing and containing the ovum or female gamete. The corresponding male organ is called the antheridium. The archegonium has a long neck canal or venter and a swollen base. Archegonia are typically located on the surface of the plant thallus, although in the hornworts they are embedded.
Protoplast, is a biological term coined by Hanstein in 1880 to refer to the entire cell, excluding the cell wall. Protoplasts can be generated by stripping the cell wall from plant, bacterial, or fungal cells by mechanical, chemical or enzymatic means.
Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids.
Recombinases are genetic recombination enzymes.
DNA repair protein RAD51 homolog 1 is a protein encoded by the gene RAD51. The enzyme encoded by this gene is a member of the RAD51 protein family which assists in repair of DNA double strand breaks. RAD51 family members are homologous to the bacterial RecA, Archaeal RadA and yeast Rad51. The protein is highly conserved in most eukaryotes, from yeast to humans.
Gene targeting is a biotechnological tool used to change the DNA sequence of an organism. It is based on the natural DNA-repair mechanism of Homology Directed Repair (HDR), including Homologous Recombination. Gene targeting can be used to make a range of sizes of DNA edits, from larger DNA edits such as inserting entire new genes into an organism, through to much smaller changes to the existing DNA such as a single base-pair change. Gene targeting relies on the presence of a repair template to introduce the user-defined edits to the DNA. The user will design the repair template to contain the desired edit, flanked by DNA sequence corresponding (homologous) to the region of DNA that the user wants to edit; hence the edit is targeted to a particular genomic region. In this way Gene Targeting is distinct from natural homology-directed repair, during which the ‘natural’ DNA repair template of the sister chromatid is used to repair broken DNA. The alteration of DNA sequence in an organism can be useful in both a research context – for example to understand the biological role of a gene – and in biotechnology, for example to alter the traits of an organism.
RAD52 homolog , also known as RAD52, is a protein which in humans is encoded by the RAD52 gene.
DNA repair and recombination protein RAD54-like is a protein that in humans is encoded by the RAD54L gene.
Meiotic recombination protein DMC1/LIM15 homolog is a protein that in humans is encoded by the DMC1 gene.
Ralf Reski is a German professor of plant biotechnology and former dean of the Faculty of Biology of the University of Freiburg. He is also affiliated to the French École supérieure de biotechnologie Strasbourg (ESBS) and Senior Fellow at the Freiburg Institute for Advanced Studies.
Sexual reproduction is a type of reproduction that involves a complex life cycle in which a gamete with a single set of chromosomes combines with another gamete to produce a zygote that develops into an organism composed of cells with two sets of chromosomes (diploid). This is typical in animals, though the number of chromosome sets and how that number changes in sexual reproduction varies, especially among plants, fungi, and other eukaryotes.
A knockout moss is one kind of genetically modified moss, which are GM plants. One or more of the moss's specific genes are deleted or inactivated, for example by gene targeting or other methods. After the deletion of a gene, the knockout moss has lost the trait encoded by this gene. Thus, the function of this gene can be inferred. This scientific approach is called reverse genetics as the scientist wants to unravel the function of a specific gene. In classical genetics the scientist starts with a phenotype of interest and searches for the gene that causes this phenotype. Knockout mosses are relevant for basic research in biology as well as in biotechnology.
The International Moss Stock Center (IMSC) is a biorepository which is specialized in collecting, preserving and distributing moss plants of a high value of scientific research. The IMSC is located at the Faculty of Biology, Department of Plant Biotechnology, at the Albert-Ludwigs-University of Freiburg, Germany.
A moss bioreactor is a photobioreactor used for the cultivation and propagation of mosses. It is usually used in molecular farming for the production of recombinant protein using transgenic moss. In environmental science moss bioreactors are used to multiply peat mosses e.g. by the Mossclone consortium to monitor air pollution.
Reverse genetics is a method in molecular genetics that is used to help understand the function(s) of a gene by analysing the phenotypic effects caused by genetically engineering specific nucleic acid sequences within the gene. The process proceeds in the opposite direction to forward genetic screens of classical genetics. While forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find what phenotypes are controlled by particular genetic sequences.
A double-strand break repair model refers to the various models of pathways that cells undertake to repair double strand-breaks (DSB). DSB repair is an important cellular process, as the accumulation of unrepaired DSB could lead to chromosomal rearrangements, tumorigenesis or even cell death. In human cells, there are two main DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR relies on undamaged template DNA as reference to repair the DSB, resulting in the restoration of the original sequence. NHEJ modifies and ligates the damaged ends regardless of homology. In terms of DSB repair pathway choice, most mammalian cells appear to favor NHEJ rather than HR. This is because the employment of HR may lead to gene deletion or amplification in cells which contains repetitive sequences. In terms of repair models in the cell cycle, HR is only possible during the S and G2 phases, while NHEJ can occur throughout whole process. These repair pathways are all regulated by the overarching DNA damage response mechanism. Besides HR and NHEJ, there are also other repair models which exists in cells. Some are categorized under HR, such as synthesis-dependent strain annealing, break-induced replication, and single-strand annealing; while others are an entirely alternate repair model, namely, the pathway microhomology-mediated end joining (MMEJ).
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