Editing Chloroplast (section)

=== Protein targeting and import ===

{{See also|Translation (biology)|label 1=Translation}}

Because so many chloroplast genes have been moved to the nucleus, many [[protein]]s that would originally have been [[Translation (biology)|translated]] in the chloroplast are now synthesized in the cytoplasm of the plant cell. These proteins must be directed back to the chloroplast, and imported through at least two chloroplast membranes.<ref name="Soll-2004">{{cite journal | vauthors=Soll J, Schleiff E | title=Protein import into chloroplasts | journal=Nature Reviews Molecular Cell Biology | volume=5 | issue=3 | pages=198–208 | date=March 2004 | pmid=14991000 | doi=10.1038/nrm1333 | s2cid=32453554 | url=http://nbn-resolving.de/urn:nbn:de:bvb:19-epub-3587-4 }}</ref>

Curiously, around half of the protein products of transferred genes aren't even targeted back to the chloroplast. Many became [[exaptations]], taking on new functions like participating in [[cell division]], [[protein routing]], and even [[disease resistance]]. A few chloroplast genes found new homes in the [[mitochondrial genome]]—most became nonfunctional [[pseudogenes]], though a few [[tRNA]] genes still work in the [[mitochondrion]].<ref name="Martin-2002" /> Some transferred chloroplast DNA protein products get directed to the [[secretory pathway]],<ref name="Martin-2002" /> though many [[#Secondary and tertiary endosymbiosis|secondary plastids]] are bounded by an outermost membrane derived from the host's [[cell membrane]], and therefore [[topologically]] outside of the cell because to reach the chloroplast from the [[cytosol]], the [[cell membrane]] must be crossed, which signifies entrance into the [[extracellular space]]. In those cases, chloroplast-targeted proteins do initially travel along the secretory pathway.<ref name="Keeling-2010" />

Because the cell acquiring a chloroplast [[#Primary endosymbiosis|already]] had [[Mitochondrion|mitochondria]] (and [[peroxisomes]], and a [[cell membrane]] for secretion), the new chloroplast host had to develop a unique [[protein targeting system]] to avoid having chloroplast proteins being sent to the wrong [[organelle]].<ref name="Soll-2004" />

{{plain image with caption|File:Tetrapeptide structural formulae.svg| The two ends of a polypeptide are called the [[N-terminus]], or ''amino end'', and the [[C-terminus]], or ''carboxyl end''.<ref name="Campbell-2009a">{{cite book | vauthors=Campbell NA, Reece JB, Urry LA, Cain ML, Wasserman, Minorsky PV, Jackson RB |title=Biology | edition=8th | year=2009 |publisher=Benjamin Cummings (Pearson) | page=340 | isbn=978-0-8053-6844-4 }}</ref> This [[polypeptide]] has four [[amino acids]] linked together. At the left is the [[N-terminus]], with its [[amino group|amino]] (H<sub>2</sub>'''N''') group in green. The blue [[C-terminus]], with its [[carboxyl group]] ('''C'''O<sub>2</sub>H) is at the right.|370px|right|bottom|triangle|#00aa15}}

In most, but not all cases, nuclear-encoded chloroplast proteins are [[Translation (biology)|translated]] with a ''[[cleavable transit peptide]]'' that's added to the N-terminus of the protein precursor. Sometimes the transit sequence is found on the C-terminus of the protein,<ref name="Lung-2012">{{cite journal | vauthors=Lung SC, Chuong SD | title=A transit peptide-like sorting signal at the C terminus directs the Bienertia sinuspersici preprotein receptor Toc159 to the chloroplast outer membrane | journal=The Plant Cell | volume=24 | issue=4 | pages=1560–78 | date=April 2012 | pmid=22517318 | pmc=3398564 | doi=10.1105/tpc.112.096248 | bibcode=2012PlanC..24.1560L }}</ref> or within the functional part of the protein.<ref name="Soll-2004" />

==== Transport proteins and membrane translocons ====

After a chloroplast [[polypeptide]] is synthesized on a [[ribosome]] in the [[cytosol]], an enzyme [[enzyme specificity|specific]] to chloroplast proteins<ref name="Waegemann-1996">{{cite journal | vauthors=Waegemann K, Soll J | title=Phosphorylation of the transit sequence of chloroplast precursor proteins | journal=The Journal of Biological Chemistry | volume=271 | issue=11 | pages=6545–54 | date=March 1996 | pmid=8626459 | doi=10.1074/jbc.271.11.6545 | doi-access=free }}</ref> [[phosphorylates]], or adds a [[phosphate group]] to many (but not all) of them in their transit sequences.<ref name="Soll-2004" />
Phosphorylation helps many proteins bind the polypeptide, keeping it from [[protein folding|folding]] prematurely.<ref name="Soll-2004" /> This is important because it prevents chloroplast proteins from assuming their active form and carrying out their chloroplast functions in the wrong place—the [[cytosol]].<ref name="May-2000" /><ref name="Jarvis-2001">{{cite journal | vauthors=Jarvis P, Soll J | title=Toc, Tic, and chloroplast protein import | journal=Biochimica et Biophysica Acta (BBA) - Molecular Cell Research | volume=1541 | issue=1–2 | pages=64–79 | date=December 2001 | pmid=11750663 | doi=10.1016/S0167-4889(01)00147-1 | doi-access=free }}</ref> At the same time, they have to keep just enough shape so that they can be recognized by the chloroplast.<ref name="May-2000">{{cite journal | vauthors=May T, Soll J | title=14-3-3 proteins form a guidance complex with chloroplast precursor proteins in plants | journal=The Plant Cell | volume=12 | issue=1 | pages=53–64 | date=January 2000 | pmid=10634907 | pmc=140214 | doi=10.1105/tpc.12.1.53 | bibcode=2000PlanC..12...53M }}</ref> These proteins also help the polypeptide get imported into the chloroplast.<ref name="Soll-2004" />

From here, chloroplast proteins bound for the stroma must pass through two protein complexes—the [[TOC complex]], or ''[[translocon|'''t'''ranslocon]] on the '''o'''uter '''c'''hloroplast membrane'', and the [[TIC translocon]], or '''''t'''ranslocon on the '''i'''nner '''c'''hloroplast membrane [[translocon]]''.<!--Yes, that's what the source says--><ref name="Soll-2004" /> Chloroplast polypeptide chains probably often travel through the two complexes at the same time, but the TIC complex can also retrieve preproteins lost in the [[chloroplast intermembrane space|intermembrane space]].<ref name="Soll-2004" />