New insights on the function of plant acyl carrier proteins from comparative and evolutionary analysis

Yang, Xiao; Liu, Xiaoxue; Zhou, Yanchen; Zhang, Fan; Huang, Lan; Wang, Jun; Jiang, Song; Qiu, Lijuan

doi:10.1016/j.ygeno.2020.11.015

Cited by 9 publications

(11 citation statements)

References 86 publications

(113 reference statements)

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“…During gene evolution, gene duplication or loss may lead to differences in the number of gene family members [ 41 ]. In this study, nine SbACPs were identified from sorghum genome by bioinformatics methods, and their physicochemical properties were predicted to be a class of acidic small molecule proteins, which was consistent with previous reports [ 42 ]. The protein length, molecular weight, and isoelectric point of SbACPs were highly conservative, whereas the number of exons varied from 2 to 4.…”

Section: Discussionsupporting

confidence: 90%

“…In Arabidopsis, ACP genes were divided into two types: plastidial ACP and mitochondrial ACP [ 35 , 42 ]. In sorghum, ACP genes were also predicted to express in chloroplast and mitochondria.…”

Section: Discussionmentioning

confidence: 99%

“…But we still could not rule out the possibility of double-localizing for several SbACP genes. On the other hand, Yang et al systematically analyzed ACP genes of 20 plant species and found that protein sequences (motifs and length) were highly conserved in different ACP branches [ 42 ]. Coincidently, Farmer et al proposed the same opinions and thought that the three-dimensional structure of the acyl carrier proteins was highly conserved, which were folded into a flexible α-helical bundle [ 42 ].…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, Yang et al systematically analyzed ACP genes of 20 plant species and found that protein sequences (motifs and length) were highly conserved in different ACP branches [ 42 ]. Coincidently, Farmer et al proposed the same opinions and thought that the three-dimensional structure of the acyl carrier proteins was highly conserved, which were folded into a flexible α-helical bundle [ 42 ]. In this study, the three-dimensional structure prediction showed the same results with the former researches.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

Hua

et al. 2022

BMC Genomics

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Background Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum. Results Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1–3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four α helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What’s more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum. Conclusions In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

Hua

et al. 2022

BMC Genomics

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“…The genetic dataset was aligned as translated amino-acids with MUSCLE3.8 available in the Aliview software [ 31 , 32 ]. The Ka/Ks ratio was then calculated with the yn00 method available in PAML [ 43 ] as previously described [ 44 ], and plotted in the R environment v.4.1.1.…”

Section: Methodsmentioning

confidence: 99%

A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates

Barbera

Cucini

2022

BMC Genomics

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Background The group XIV of C-type lectin domain-containing proteins (CTLDcps) is one of the seventeen groups of CTLDcps discovered in mammals and composed by four members: CD93, Clec14A, CD248 and Thrombomodulin, which have shown to be important players in cancer and vascular biology. Although these proteins belong to the same family, their phylogenetic relationship has never been dissected. To resolve their evolution and characterize their protein domain composition we investigated CTLDcp genes in gnathostomes and cyclostomes and, by means of phylogenetic approaches as well as synteny analyses, we inferred an evolutionary scheme that attempts to unravel their evolution in modern vertebrates. Results Here, we evidenced the paralogy of the group XIV of CTLDcps in gnathostomes and discovered that a gene loss of CD248 and Clec14A occurred in different vertebrate groups, with CD248 being lost due to chromosome disruption in birds, while Clec14A loss in monotremes and marsupials did not involve chromosome rearrangements. Moreover, employing genome annotations of different lampreys as well as one hagfish species, we investigated the origin and evolution of modern group XIV of CTLDcps. Furthermore, we carefully retrieved and annotated gnathostome CTLDcp domains, pointed out important differences in domain composition between gnathostome classes, and assessed codon substitution rate of each domain by analyzing nonsynonymous (Ka) over synonymous (Ks) substitutions using one representative species per gnathostome order. Conclusions CTLDcps appeared with the advent of early vertebrates after a whole genome duplication followed by a sporadic tandem duplication. These duplication events gave rise to three CTLDcps in the ancestral vertebrate that underwent further duplications caused by the independent polyploidizations that characterized the evolution of cyclostomes and gnathostomes. Importantly, our analyses of CTLDcps in gnathostomes revealed critical inter-class differences in both extracellular and intracellular domains, which might help the interpretation of experimental results and the understanding of differences between animal models.

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Genome-wide analysis of Triticum aestivum bromodomain gene family and expression analysis under salt stress

Wang,

Shen,

et al. 2024

Planta

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New insights on the function of plant acyl carrier proteins from comparative and evolutionary analysis

Cited by 9 publications

References 86 publications

Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench

A glimpse into the past: phylogenesis and protein domain analysis of the group XIV of C-type lectins in vertebrates

Genome-wide analysis of Triticum aestivum bromodomain gene family and expression analysis under salt stress

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