Editing Plastid (section)

===Plastomes and Chloroplast DNA/ RNA; plastid DNA and plastid nucleoids===

Each plastid creates multiple copies of its own unique genome, or [[plastome]], (from 'plastid genome'){{mdash}}which for a chlorophyll plastid (or chloroplast) is equivalent to a 'chloroplast genome', or a 'chloroplast DNA'.<ref>{{cite journal |last1=Wicke |first1=S |last2=Schneeweiss |first2=GM |last3=dePamphilis |first3=CW |last4=Müller |first4=KF |last5=Quandt |first5=D |title=The evolution of the plastid chromosome in land plants: gene content, gene order, gene function |journal=Plant Molecular Biology |date=2011 |volume=76 |issue=3–5 |pages=273–297 |doi=10.1007/s11103-011-9762-4 |pmid=21424877 |pmc=3104136 |doi-access=free |bibcode=2011PMolB..76..273W }}</ref><ref>{{cite journal |last1=Wicke |first1=S |last2=Naumann |first2=J |title=Molecular evolution of plastid genomes in parasitic flowering plants |journal=Advances in Botanical Research |date=2018 |volume=85 |pages=315–347 |doi=10.1016/bs.abr.2017.11.014 |isbn=9780128134573 |url=https://www.sciencedirect.com/science/article/pii/S0065229617300861}}</ref> The number of genome copies produced per plastid is variable, ranging from 1000 or more in [[cell division|rapidly dividing new cells]], encompassing only a few plastids, down to 100 or less in mature cells, encompassing numerous plastids.

A plastome typically contains a [[genome]] that encodes ''transfer'' [[ribonucleic acid]]s ([[tRNA]])s and ''ribosomal'' [[ribonucleic acid]]s ([[rRNA]]s). It also contains proteins involved in photosynthesis and plastid gene [[Transcription (genetics)|transcription]] and [[Translation (biology)|translation]]. But these proteins represent only a small fraction of the total protein set-up necessary to build and maintain any particular type of plastid. [[Cell nucleus|Nuclear]] genes (in the cell nucleus of a plant) encode the vast majority of plastid proteins; and the expression of nuclear and plastid genes is co-regulated to coordinate the development and [[cell differentiation|differention]] of plastids.

Many plastids, particularly those responsible for photosynthesis, possess numerous internal membrane layers. Plastid DNA exists as protein-DNA complexes associated as localized ''regions'' within the plastid's inner envelope [[Inner nuclear membrane|membrane]]; and these complexes are called 'plastid [[nucleoid]]s'. Unlike the nucleus of a eukaryotic cell, a plastid nucleoid is ''not'' surrounded by a nuclear membrane. The region of each nucleoid may contain more than 10 copies of the plastid DNA.

Where the proplastid (''undifferentiated plastid'') contains a single nucleoid region located near the centre of the proplastid, the ''developing (or differentiating) plastid'' has many nucleoids localized at the periphery of the plastid and bound to the inner envelope membrane. During the development/ differentiation of proplastids to chloroplasts{{mdash}}and when plastids are differentiating from one type to another{{mdash}}nucleoids change in morphology, size, and location within the organelle. The remodelling of plastid nucleoids is believed to occur by modifications to the abundance of and the composition of nucleoid proteins.

In normal [[plant cell]]s long thin protuberances called [[stromule]]s sometimes form{{mdash}}extending from the plastid body into the cell [[cytosol]] while interconnecting several plastids. Proteins and smaller molecules can move around and through the stromules. Comparatively, in the laboratory, most cultured cells{{mdash}}which are large compared to normal plant cells{{mdash}}produce very long and abundant stromules that extend to the cell periphery.

In 2014, evidence was found of the possible loss of plastid genome in ''[[Rafflesia]] lagascae'', a non-photosynthetic [[Parasitism|parasitic]] flowering plant, and in ''[[Polytomella]]'', a genus of non-photosynthetic [[green algae]]. Extensive searches for plastid genes in both [[taxon]]s yielded no results, but concluding that their plastomes are entirely missing is still disputed.<ref name="The Scientist">{{Cite web|title = Plants Without Plastid Genomes|url = https://www.the-scientist.com/plants-without-plastid-genomes-37895|website = The Scientist|access-date = 2015-09-26}}</ref> Some scientists argue that plastid genome loss is unlikely since even these non-photosynthetic plastids contain genes necessary to complete various [[Biosynthesis|biosynthetic pathways]] including heme biosynthesis.<ref name="The Scientist" /><ref>{{cite journal | vauthors = Barbrook AC, Howe CJ, Purton S | title = Why are plastid genomes retained in non-photosynthetic organisms? | journal = Trends in Plant Science | volume = 11 | issue = 2 | pages = 101–8 | date = February 2006 | pmid = 16406301 | doi = 10.1016/j.tplants.2005.12.004 }}</ref>

Even with any loss of plastid genome in [[Rafflesiaceae]], the plastids still occur there as "shells" without DNA content,<ref name="NoDNA">{{cite web|title =DNA of Giant 'Corpse Flower' Parasite Surprises Biologists|url=https://www.quantamagazine.org/dna-of-giant-corpse-flower-parasite-surprises-biologists-20210421/| date =April 2021}}</ref> which is reminiscent of [[hydrogenosome]]s in various organisms.