Cider Musings

Development of Pome Fruit : Genetics and Biochemistry.



In botany, a pome is a type of fruit produced by flowering plants  of the tribe Malineae  of the very large family Rosaceae. It is a false fruit.

This is only  group that  form fruits like this. And they have a curious chromosomal count  of 17  rather than 7-9 chromosomes that  the rest of Rosaceae species have. All these 17 chromosomes are derived from the original 7 with much duplication of some whole chromosomes,  parts of chromosomes, and some deleted and moved or crossed over segments of chromosomes.


Expansion of the gene segments of the chromosomes responsible for fruit formation gives the pome species a false fruit. Expansion of the chromosomes responsible for sorbitol metabolism gives the pome species the power to fill the large fruits with sugars. So the apple that resulted has a large fruit filled with sugars. An ecological  niche that attracts large mammals such as bears and deer.


By tracing genome alterations over time, this genome wide duplication event has been dated  to around 60 +/- 10 million years ago and timed with the climate destruction caused by the dinosaur extinction asteroid impact.  It occurred only in this tribe, which is spread around the world; in apples, pears, medlars, hawthorn and loquats to name the most common. Why pome species convert glucose into sorbitol to transport to sink tissues - roots and fruits, rather than the usual sucrose is unclear. Perhaps they evolved new uses,  caused by the expanded genes from the likely earliest use of regulating osmolality and turgidity of structures, (sorbitol is important in draught resistance in plant species from algae to trees). Interestingly it did not occur in another plant group poplar trees that also underwent wide genome duplication at the same time.


Sorbitol is literally the life blood of these plants several orders more sorbitol is transported than sucrose the most common sugar transported in plants.  It is synthesised in and flows from the leaves to nourish the rest of the plant and is stored in the fruits to entice seed dispersal animals with sweet tastes.


However let’s recap the first phase of sugar production in plants from photosynthesis that occurs across all plant species. Fifty years ago, the biochemist Dr. Melvin Calvin figured out the photosynthetic process from his lab at the University of California at Berkeley, USA and the Calvin cycle is named after him. He worked in a wooden building at Berkeley called the Old Radiation Lab, a fact as a radiologist I rather like. Calvin studied the application of light on carbon 14 metabolism in green algae and traced its path through the algae’s chloroplast, from CO2 to glucose. This is a cyclical process which can be thought of as a mirror image of the Krebs cycle - the process of releasing energy from sugar. Here energy from sunlight is captured into glucose, which is then converted into sucrose for transport in most plants.


In this discussion on pome fruit metabolism this glucose is then converted mainly into sorbitol in pome species  leaf cells  mitochondria by  glucose 6-phosphate by NADP-dependent sorbitol-6-phosphate dehydrogenase - S6PDH for  transport to the rest of the plant.   The transportation of both sucrose and sorbitol occurs from leaves to fruits through the phloem with the aid of an active sorbitol specific cell wall transporter - SOT in phloem cells. 


The enzyme sorbitol dehydrogenase ( abbreviated to SDH ) is used to regulate sorbitol and its end products is commonly found in all kinds of life forms, including animals, yeasts , bacteria and plants to control the effects of climate stress such as drought being an osmotic chemical. It is over expressed in the group pomes, eg   apples and pears, the trees that  have these large pome fruits.  This enzyme then  converts  sorbitol back to sugars in the apple fruit for storage.


Primer - Enzymes such as SDH facilitate metabolic processes such as the conversion of sorbitol into glucose.  Every day, trillions upon trillions of chemical reactions occur in living cells  to make essential metabolic processes occur. Enzymes are molecules made of amino acids that act upon substrate molecules and decrease the activation energy necessary for a chemical reaction to occur thus  speeding up the reaction rates. At the core of these reactions is  NAD+ (nicotinamide adenine dinucleotide)  This compound is made of adenosine one one the  building blocks as DNA. While DNA is made up of billions of nucleotides, NAD+ is rather small – composed of just two!   This can be transformed into NADH which is very similar to NAD+, the only difference being it’s a hydride. (A hydride is a hydrogen atom with an extra electron -  a neutrally charged hydrogen atom holding on to a negatively charged electron). This gives NADH an overall negative charge. NAD+ is an electron carrier because it carries the electrons of a hydride from one region of a cell to another as a stable shuttle molecule.  This process of moving electrons around makes NAD+ and NADH oxidation-reduction, or “redox” molecules.  This process is very  repeatable so that NAD+ can continuously gain and lose electrons, and is mobile so is an effective electron carrier. 

Enzymes are made built into complex 3 D structures that often contain a metal and the case of SDH, zinc. This shape cocoons the substate eg sorbitol whist it is converted, the process being powered by energy exchange by H+ ions. There are several families of enzymes that have evolved from unicellular organisms right through to advanced plants such as the apple and animals. SDH represents the early enzyme within the NAD (H)-dependent medium-chain dehydrogenase/reductase group - MDR superfamily, co-incidently sharing a distant homology with alcohol dehydrogenase (ADH, the other enzyme of major importance in cider and other alcoholic drinks.


A lot is known about the structure of these enzymes now due to advances in X ray crystallography . When I studied biochemistry and physiology enzymes were a ‘black box’. SDH catalyses the reversible oxidation of a range of related sugar alcohols into their corresponding sugar ketoses, here sorbitol into fructose. The process of sorbitol oxidation  requires firstly NAD+ ( energy packet) to bind the specific enzyme  protein site followed by the sorbitol molecule . The backbone of sorbitol stacks against the nicotinamide ring while the C1 and C2 oxygen atoms are coordinated to the zinc. A water molecule coordinating the zinc atom acts a general base and abstracts the proton of the C2 hydroxyl, which creates an electron flow to NAD+, leading to the oxidation of sorbitol at C2 to form a ketone group C=O and the production of NADH by its reduction.


In pome species SDH also plays a crucial role  of sorbitol metabolism in the early  developing fruits. Gene transcript level and enzyme activity remain high during fruit development and maturation, dropping gradually in later stages, and contributing to the sugar accumulation in the ripening fruits. We are lucky to know this, a lot of work has been done here given the economic importance of apples and pears. 


However little attention has been given to the evolutionary history of the plant SDH gene family that controls the enzymes . The distribution of the SDH genes in higher plants is  species-dependant. In particular, 9 paralogous SDH genes have been reported in the apple from its dramatically increased chromosomal duplication and rearrangement that occurred at the dinosaur extinction event 66 million years ago, that lead to this  new group of Malinae or pome fruits.  There is only a single gene locus in non Rosaceae tree species such as oak which transports mainly sugars in the phloem sap.


There is however this interesting paper which investigated  differences in gene family size between pomes and non sorbitol dominant control fruits, tomato, and poplar. There are five enzymes and one transporter that are closely related to the biosynthesis, degradation and transportation of sorbitol in plants and these to varying degrees are linked to over expression of genes on the Malineae sub tribe from chromosomal duplication. The identified genes in the S6PDHSDH and SOT families were compared. In total, 20 S6PDH, 33 SDH and 59 SOT genes were identified. In these gene families, the average gene numbers in pomes was 4.0 for S6PDH, 7.5 for SDH and 13.75 for SOT ie  larger than those in the control group 1.3 for S6PDH, 1.0 for SDH and 1.3 for SOT, indicating gene family size expansion is contributing to the evolution of the sorbitol character. Although the gene numbers in pear and apple are constantly larger than those in the control group, this is not the case for the S6PDH and SDH genes in peach and mei, which have similar or identical gene numbers, that is one or two.

This indicated that gene family size expansion did not necessarily happen in all three gene families.equally which would be logical given the complex nature of the chromosomal changes which would have occurred in several stages over millennia.  This paper describes it in more detail. Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants. L Li et al.

So the dinosaurs loss was our gain. This rapid ( in evolutionary terms) evolution of new species of the Malineae trees is an example of adaptive radiation which occurs when new niches open up occurred through a genome wide expansion which occurred after the major climate change that occurred from the asteroid impact 66 M years ago.