Chloroplast Division in Higher Plants Requires Members of Two Functionally Divergent Gene Families with Homology to Bacterial ftsZ

FtsZ is a key protein involved in bacterial and organellar division. Bacteria have only one ftsZ gene, while chlorophytes (higher plants and green alga) have two distinct FtsZ gene families, named FtsZ1 and FtsZ2. This raises the question of why chloroplasts in these organisms need distinct FtsZ proteins to divide. In order to unravel new functions associated with FtsZ proteins, we have identified and characterized an Arabidopsis thaliana FtsZ1 loss-of-function mutant. ftsZ1-knockout mutants are impeded in chloroplast division, and division is restored when FtsZ1 is expressed at a low level. FtsZ1-overexpressing plants show a drastic inhibition of chloroplast division. Chloroplast morphology is altered in ftsZ1, with chloroplasts having abnormalities in the thylakoid membrane network. Overexpression of FtsZ1 also induced defects in thylakoid organization with an increased network of twisting thylakoids and larger grana. We show that FtsZ1, in addition to being present in the stroma, is tightly associated with the thylakoid fraction. This association is developmentally regulated since FtsZ1 is found in the thylakoid fraction of young developing plant leaves but not in mature and old plant leaves. Our results suggest that plastid division protein FtsZ1 may have a function during leaf development in thylakoid organization, thus highlighting new functions for green plastid FtsZ.

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Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

BMC Plant Biology ◽

10.1186/s12870-021-02872-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Zihan Cheng ◽

Xuemei Zhang ◽

Wenjing Yao ◽

Kai Zhao ◽

Lin Liu ◽

...

Keyword(s):

Gene Family ◽

Higher Plants ◽

Abiotic Stress Tolerance ◽

Gene Families ◽

Regulatory Elements ◽

Late Embryogenesis Abundant ◽

Genome Wide ◽

Lea Gene ◽

Late Embryogenesis ◽

Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

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Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Horticulture Research ◽

10.1038/s41438-021-00562-7 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Xiaoming Song ◽

Qihang Yang ◽

Yun Bai ◽

Ke Gong ◽

Tong Wu ◽

...

Keyword(s):

Higher Plants ◽

Extreme Environments ◽

Gene Families ◽

Comprehensive Analysis ◽

Whole Genome ◽

Flowering Genes ◽

Database Construction ◽

Myb Gene ◽

Gene Coding ◽

Lower Plants

AbstractSimple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/. We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

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Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽

10.3390/plants9101356 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1356

Author(s):

Zhaohan Zhang ◽

Shahid Ali ◽

Tianxu Zhang ◽

Wanpeng Wang ◽

Linan Xie

Keyword(s):

Gene Family ◽

Higher Plants ◽

Expression Patterns ◽

Family Members ◽

Evolutionary Relationship ◽

Gene Families ◽

Class Iii ◽

Sequencing Data ◽

Entire Genome ◽

Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

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Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants

10.1101/867242 ◽

2019 ◽

Author(s):

Ryan W. Christian ◽

Seanna L. Hewitt ◽

Eric H. Roalson ◽

Amit Dhingra

Keyword(s):

Panicum Virgatum ◽

Higher Plants ◽

Gene Families ◽

Transcript Abundance ◽

Arabidopsis Proteome ◽

Genome Wide ◽

Plastid Targeting ◽

Wide Scale ◽

Scale Characterization ◽

Angiosperm Species

AbstractPlastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. Between 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to change plastid morphology and biochemistry.

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OBSERVATIONS ON THE MECHANISM OF CHLOROPLAST DIVISION IN HIGHER PLANTS

New Phytologist ◽

10.1111/j.1469-8137.1981.tb01686.x ◽

1981 ◽

Vol 87 (1) ◽

pp. 1-9 ◽

Cited By ~ 52

Author(s):

RACHEL M. LEECH ◽

W. W. THOMSON ◽

K. A. PLATT-ALOIA

Keyword(s):

Higher Plants ◽

Chloroplast Division

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Egr-1, a master switch coordinating upregulation of divergent gene families underlying ischemic stress

Nature Medicine ◽

10.1038/82168 ◽

2000 ◽

Vol 6 (12) ◽

pp. 1355-1361 ◽

Cited By ~ 338

Author(s):

Shi-Fang Yan ◽

Tomoyuki Fujita ◽

Jiesheng Lu ◽

Kenji Okada ◽

Yu Shan Zou ◽

...

Keyword(s):

Gene Families ◽

Divergent Gene ◽

Ischemic Stress

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Two Tcp-1-related but highly divergent gene families exist in oat encoding proteins of assumed chaperone function

FEBS Letters ◽

10.1016/0014-5793(93)80827-h ◽

1993 ◽

Vol 336 (2) ◽

pp. 313-316 ◽

Cited By ~ 16

Author(s):

Bruno Ehmann ◽

Martina Krenz ◽

Eckart Mummert ◽

Eberhard Schäfer

Keyword(s):

Gene Families ◽

Chaperone Function ◽

Divergent Gene

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Ftsz Ring Formation at the Chloroplast Division Site in Plants

The Journal of Cell Biology ◽

10.1083/jcb.153.1.111 ◽

2001 ◽

Vol 153 (1) ◽

pp. 111-120 ◽

Cited By ~ 166

Author(s):

Stanislav Vitha ◽

Rosemary S. McAndrew ◽

Katherine W. Osteryoung

Keyword(s):

Cell Division ◽

Fluorescent Protein ◽

Higher Plants ◽

Chloroplast Division ◽

Ring Formation ◽

Protein Fusion ◽

Cell Recruitment ◽

Division Site ◽

Filament Networks ◽

Green Fluorescent

Among the events that accompanied the evolution of chloroplasts from their endosymbiotic ancestors was the host cell recruitment of the prokaryotic cell division protein FtsZ to function in chloroplast division. FtsZ, a structural homologue of tubulin, mediates cell division in bacteria by assembling into a ring at the midcell division site. In higher plants, two nuclear-encoded forms of FtsZ, FtsZ1 and FtsZ2, play essential and functionally distinct roles in chloroplast division, but whether this involves ring formation at the division site has not been determined previously. Using immunofluorescence microscopy and expression of green fluorescent protein fusion proteins in Arabidopsis thaliana, we demonstrate here that FtsZ1 and FtsZ2 localize to coaligned rings at the chloroplast midpoint. Antibodies specific for recognition of FtsZ1 or FtsZ2 proteins in Arabidopsis also recognize related polypeptides and detect midplastid rings in pea and tobacco, suggesting that midplastid ring formation by FtsZ1 and FtsZ2 is universal among flowering plants. Perturbation in the level of either protein in transgenic plants is accompanied by plastid division defects and assembly of FtsZ1 and FtsZ2 into filaments and filament networks not observed in wild-type, suggesting that previously described FtsZ-containing cytoskeletal-like networks in chloroplasts may be artifacts of FtsZ overexpression.

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