背景：在高等植物中，光合碳同化主要有3种类型：C3途径，C4途径和景天酸代谢途径(Crassulaceanacid metabolism /CAM)。在光合过程中，最重要的pathway是C固定过程，如图4。C3植物中，CO2的固定1，5-二磷酸核酮糖羧化酶(RuBPC)，它催化1，5-二磷酸核酮糖(RuBP)羧化，将大气中的CO2同化，产生两分子磷酸甘油酸。与C3植物不一样， C4植物固定CO2的酶为磷酸烯醇式丙酮酸羧化酶(PEPCase/PEPC)。PEPC酶与C3作物中RuBPC酶相比，PEPC酶对CO2的亲和力高。CAM植物与C4植物固定与还原CO2的途径基本相同，固定CO2是PEPC酶。二者的差别在于：C4植物是在同一时间(白天)和不同的空间(叶肉细胞和维管束鞘细胞)完成CO2固定(C4途径)和还原(C3途径)两个过程；而CAM植物则是在不同时间(黑夜和白天)和同一空间(叶肉细胞)完成上述两个过程的。因此，CAM植物能避开辐射和蒸腾势很高的白天，在夜晚打开气孔来吸收光合作用所需的CO2，从使它的蒸腾比远低于其它类型的植物。

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我们文章的主要结果是：

兰科CAM代谢的分子调控机制和起源研究。

CAM是从C3演化而来，是如何产生这种新的光合作用方式，很值得研究。CAM代谢 也是研究 基因新功能一个好的对象。

相对于C3和C4，CAM代谢的分子水平研究较少，已有CAM植物基因组被测序，有必要在转录组和基因组层次研究CAM的分子调控机制。对CAM代谢相关基因家族进行比较基因组和转录组学发现CAM起源可能是通过基因表达重塑起源的，即相关基因产生新功能不是通过基因重复后产生新功能，可能是建立新调控网络产生新功能。

SignificanceStatement

Crassulacean acidmetabolism (CAM) photosynthesis maximizes water use efficiency relative to C3and C4 photosynthesis, butits origin and evolution are poorlyunderstood. Here we analyzed transcriptomes of numerous orchid species tocompare carbon fixation pathway genes, and propose that CAM likely originatedby modulating existing key genes.

Summary

CAM photosynthesisis a CO₂ fixation pathway that maximizes water use efficiency (WUE)compared to the C3/C4 CO₂ pathway, which permits CAM plants to adaptto arid environments. The CAM pathway provides excellent opportunities togenetically design plants, especially bioenergy crops, with a high WUE andbetter photosynthetic performance than C3/C4 in arid environments. However, theavailable information on the origin and evolution of CAM is scant. Here, weanalyzed transcriptomes from 13 orchid species and two existing orchid genomes, covering CAM and C3 plants, with an emphasis on comparing 13 gene families involved in the complete carbon fixation pathway. The dosage of the corephotosynthesis related genes plays no substantial role in the evolution of CAM in orchids. However, CAM may have evolved primarily by changes at thetranscription level of key carbon fixation pathway genes. We proposed that inboth dark and light, CO₂ is primarily fixed and then releasedthrough two metabolic pathways via known genes, such as PPC1, PPDKand PPCK. This study reports a comprehensive comparison of carbonfixation pathway genes across different photosynthetic plants, and reveals the importance of the level of expression of key genes in the origin and evolutionof CAM.

CAM 方面已经累计了一些研究成果：

1.  参与了石斛基因组工作，石斛是能C3又能CAM

The Dendrobium catenatum Lindl. genome sequence provides insights into

polysaccharide synthase, floral development and adaptive evolution. Sci Rep. 2016 Jan 12;6:19029. doi: 10.1038/srep19029.

Zhang GQ(1), Xu Q(2), Bian C(3), Tsai WC(4,)(5,)(6), Yeh CM(7), Liu KW(8),

Yoshida K(9), Zhang LS(10), Chang SB(4), Chen F(11), Shi Y(1,)(12), Su

YY(1,)(12), Zhang YQ(1), Chen LJ(1), Yin Y(1), Lin M(1), Huang H(1), Deng H(13),

Wang ZW(14), Zhu SL(14), Zhao X(14), Deng C(14), Niu SC(2), Huang J(1), Wang

M(1), Liu GH(1), Yang HJ(1,)(12), Xiao XJ(1), Hsiao YY(5), Wu WL(1,)(5), Chen

YY(4,)(5), Mitsuda N(15), Ohme-Takagi M(7,)(15), Luo YB(2), Van de Peer

Y(16,)(17,)(18), Liu ZJ(1,)(8,)(12).

Orchids make up about 10% of all seed plant species, have great economical value,

and are of specific scientific interest because of their renowned flowers and

ecological adaptations. Here, we report the first draft genome sequence of a

lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes,

and find evidence of a whole genome duplication shared with Phalaenopsis. We

observed the expansion of many resistance-related genes, suggesting a powerful

immune system responsible for adaptation to a wide range of ecological niches. We

also discovered extensive duplication of genes involved in glucomannan synthase

activities, likely related to the synthesis of medicinal polysaccharides.

Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the

regulation of development and growth, suggests that these expansions are

associated with the astonishing diversity of plant architecture in the genus

Dendrobium. On the contrary, members of the type I MADS box gene family are

missing, which might explain the loss of the endospermous seed. The findings

reported here will be important for future studies into polysaccharide synthesis,

adaptations to diverse environments and flower architecture of Orchidaceae.

PMCID: PMC4709516

PMID: 26754549  [PubMed - in process]

2.

Evolutionary history of PEPC genes in green plants: Implications for the

evolution of CAM in orchids. Mol Phylogenet Evol. 2016 Jan;94(Pt B):559-64.

Deng H#, Zhang LS#, Zhang GQ(2), Zheng BQ(3), Liu ZJ(4), Wang Y(5).

The phosphoenolpyruvate carboxylase (PEPC) gene is the key enzyme in CAM and C4

photosynthesis. A detailed phylogenetic analysis of the PEPC family was performed

using sequences from 60 available published plant genomes, the Phalaenopsis

equestris genome and RNA-Seq of 15 additional orchid species. The PEPC family

consists of three distinct subfamilies, PPC-1, PPC-2, and PPC-3, all of which

share a recent common ancestor in chlorophyte algae. The eudicot PPC-1 lineage

separated into two clades due to whole genome duplication (WGD). Similarly, the

monocot PPC-1 lineage also divided into PPC-1M1 and PPC-1M2 through an ancient

duplication event. The monocot CAM- or C4-related PEPC originated from the clade

PPC-1M1. WGD may not be the major driver for the performance of CAM function by

PEPC, although it increased the number of copies of the PEPC gene. CAM may have

evolved early in monocots, as the CAM-related PEPC of orchids originated from the

monocot ancient duplication, and the earliest CAM-related PEPC may have evolved

immediately after the diversification of monocots, with CAM developing prior to

C4. Our results represent the most complete evolutionary history of PEPC genes in

green plants to date and particularly elucidate the origin of PEPC in orchids.

Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

PMID: 26493226  [PubMed - in process]

Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway.

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