Subfunctionalization of phytochrome B1/B2 leads to differential auxin and photosynthetic responses

Abstract

Gene duplication and polyploidization are genetic mechanisms that instantly add genetic material to an organism's genome. Subsequent modification of the duplicated material leads to the evolution of neofunctionalization (new genetic functions), subfunctionalization (differential retention of genetic functions), redundancy, or a decay of duplicated genes to pseudogenes. Phytochromes are light receptors that play a large role in plant development. They are encoded by a small gene family that in tomato is comprised of five members: PHYA, PHYB1, PHYB2, PHYE, and PHYF. The most recent gene duplication within this family was in the ancestral PHYB gene. Using transcriptome profiling, co‐expression network analysis, and physiological and molecular experimentation, we show that tomato SlPHYB1 and SlPHYB2 exhibit both common and non‐redundant functions. Specifically, PHYB1 appears to be the major integrator of light and auxin responses, such as gravitropism and phototropism, while PHYB1 and PHYB2 regulate aspects of photosynthesis antagonistically to each other, suggesting that the genes have subfunctionalized since their duplication.

Phytochrome F mediates red light responsiveness additively with phytochromes B1 and B2 in tomato

“…Interestingly, SlphyA also reduces the elongation of shoot length of seedlings grown in the dark, possibly by using phyA activated in the embryo while still on the mother plant ( Carlson et al, 2019 ). Taken together, SlPHYA , SlPHYB1 , and SlPHYB2 have distinct roles for some responses, while showing genetic redundancy in others ( Kendrick et al, 1994 , 1997 ; Quail, 1997 ; Smith and Whitelam, 1997 ; Weller et al, 2000 ; Carlson et al, 2020 ).…”

“…SlPHYB2 appears to play a role in early seedling development ( Hauser et al, 1998 ), and in cooperation with SlPHYA and SlPHYB1, in the control of de-etiolation ( Weller et al, 2000 ). Our recently published work ( Carlson et al, 2020 ) shows that SlPHYB1 and SlPHYB2 have both unique and redundant functions, for example in the regulation of photosynthetic activity (antagonistic), gravitropic and phototropic (unique) responses, and adventitious root formation (redundant). Like Arabidopsis, tomato has a PHYA gene that mediates responses to FR ( van Tuinen et al, 1995a ; Shichijo et al, 2001 ).…”

Functions of Plant Phytochrome Signaling Pathways in Adaptation to Diverse Stresses

“…Changes in light signals induce differential accumulation of phytochromes, while HIL hinders the synthesis and accumulation of chlorophyll and carotenoids, thereby regulating the photosynthetic system of tea plants under high light conditions [180]. In tomato, PHYB1 and PHYB2 antagonistically regulate various aspects of photosynthesis [181]. The phyA mutant of tomato showed reduced photosynthetic activity of the excised chloroplasts and decreased biomass in adult plants [179].…”

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

“…For example, in mammals, the Agouti-melanocortin system is represented by the Agouti protein (ASIP) and the Agouti-related protein (AgRP) whose expression patterns with distinct physiologic functions were acquired through sub-functionalization such that the current expression pattern and function of each protein correspond to a subset of the ancestral gene [ 95 ]. In tomato, two members of the gene family encoding phytochromes, which are light receptors playing a role in plant development, exhibit both common and non-redundant functions suggesting that they have sub-functionalized since their duplication [ 96 ]. Finally, it is also possible for the two copies of a gene to be both maintained in the genome by dosage subfunctionalization, each expressing the ancestral function, leading to a functional redundancy [ 97 , 98 ].…”